From d462e023efdf9d7f3f38ba6f7b5047b082585cc6 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 2 Mar 2024 21:12:41 +0100 Subject: [PATCH] oh Picard ... --- tools/picard/picard_AddCommentsToBam.xml | 12 ++--- .../picard/picard_AddOrReplaceReadGroups.xml | 26 ++++----- tools/picard/picard_BedToIntervalList.xml | 10 ++-- tools/picard/picard_CleanSam.xml | 10 ++-- .../picard_CollectAlignmentSummaryMetrics.xml | 22 ++++---- .../picard_CollectBaseDistributionByCycle.xml | 22 ++++---- tools/picard/picard_CollectGcBiasMetrics.xml | 24 ++++----- tools/picard/picard_CollectHsMetrics.xml | 22 ++++---- .../picard_CollectInsertSizeMetrics.xml | 24 ++++----- tools/picard/picard_CollectRnaSeqMetrics.xml | 24 ++++----- ...card_CollectSequencingArtifactsMetrics.xml | 30 +++++------ tools/picard/picard_CollectWgsMetrics.xml | 18 +++---- tools/picard/picard_DownsampleSam.xml | 14 ++--- .../picard_EstimateLibraryComplexity.xml | 26 ++++----- tools/picard/picard_FastqToSam.xml | 54 +++++++++---------- tools/picard/picard_FilterSamReads.xml | 28 +++++----- tools/picard/picard_FixMateInformation.xml | 16 +++--- tools/picard/picard_MarkDuplicates.xml | 31 +++++------ .../picard_MarkDuplicatesWithMateCigar.xml | 31 +++++------ tools/picard/picard_MeanQualityByCycle.xml | 20 +++---- tools/picard/picard_MergeBamAlignment.xml | 52 +++++++++--------- tools/picard/picard_MergeSamFiles.xml | 20 +++---- tools/picard/picard_NormalizeFasta.xml | 12 ++--- .../picard_QualityScoreDistribution.xml | 26 ++++----- tools/picard/picard_ReorderSam.xml | 26 ++++----- tools/picard/picard_ReplaceSamHeader.xml | 10 ++-- ...rtOriginalBaseQualitiesAndAddMateCigar.xml | 16 +++--- tools/picard/picard_RevertSam.xml | 28 +++++----- tools/picard/picard_SamToFastq.xml | 36 ++++++------- tools/picard/picard_SortSam.xml | 12 ++--- tools/picard/picard_ValidateSamFile.xml | 22 ++++---- 31 files changed, 364 insertions(+), 360 deletions(-) diff --git a/tools/picard/picard_AddCommentsToBam.xml b/tools/picard/picard_AddCommentsToBam.xml index 6a7d3010196..6afcf22fbe8 100644 --- a/tools/picard/picard_AddCommentsToBam.xml +++ b/tools/picard/picard_AddCommentsToBam.xml @@ -15,14 +15,14 @@ picard AddCommentsToBam - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' #for $element in $comments: - -COMMENT '${element.comment}' + --COMMENT '${element.comment}' #end for - -QUIET true - -VERBOSITY ERROR - -VALIDATION_STRINGENCY ${validation_stringency} + --QUIET true + --VERBOSITY ERROR + --VALIDATION_STRINGENCY ${validation_stringency} ]]> diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml index ff379e14f0c..61711b83675 100644 --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -13,19 +13,19 @@ @java_options@ @symlink_element_identifier@ picard AddOrReplaceReadGroups - -INPUT '$escaped_element_identifier' - $format_read_group("-RGLB ", $rg_lb, '"') - $format_read_group("-RGPL ", $rg_pl, '"') - $format_read_group("-RGPU ", $rg_pu, '"') - $format_read_group("-RGSM ", $rg_sm, '"') - $format_read_group("-RGID ", $rg_id, '"') - $format_read_group("-RGDS ", $rg_ds, '"') - $format_read_group("-RGPI ", $rg_pi, '"') - $format_read_group("-RGDT ", $rg_dt, '"') - -OUTPUT '${outFile}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + $format_read_group("--RGLB ", $rg_lb, '"') + $format_read_group("--RGPL ", $rg_pl, '"') + $format_read_group("--RGPU ", $rg_pu, '"') + $format_read_group("--RGSM ", $rg_sm, '"') + $format_read_group("--RGID ", $rg_id, '"') + $format_read_group("--RGDS ", $rg_ds, '"') + $format_read_group("--RGPI ", $rg_pi, '"') + $format_read_group("--RGDT ", $rg_dt, '"') + --OUTPUT '${outFile}' + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_BedToIntervalList.xml b/tools/picard/picard_BedToIntervalList.xml index 47180c3aedd..dff29c447a6 100644 --- a/tools/picard/picard_BedToIntervalList.xml +++ b/tools/picard/picard_BedToIntervalList.xml @@ -32,12 +32,12 @@ picard BedToIntervalList - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' - -SEQUENCE_DICTIONARY '${picard_dict}' - -QUIET true - -VERBOSITY ERROR + --SEQUENCE_DICTIONARY '${picard_dict}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CleanSam.xml b/tools/picard/picard_CleanSam.xml index e539c6894e0..17996aec2b1 100644 --- a/tools/picard/picard_CleanSam.xml +++ b/tools/picard/picard_CleanSam.xml @@ -9,11 +9,11 @@ @java_options@ @symlink_element_identifier@ picard CleanSam - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -QUIET true - -VERBOSITY ERROR - -VALIDATION_STRINGENCY ${validation_stringency} + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --QUIET true + --VERBOSITY ERROR + --VALIDATION_STRINGENCY ${validation_stringency} ]]> diff --git a/tools/picard/picard_CollectAlignmentSummaryMetrics.xml b/tools/picard/picard_CollectAlignmentSummaryMetrics.xml index eec90ab5164..12da48c1193 100644 --- a/tools/picard/picard_CollectAlignmentSummaryMetrics.xml +++ b/tools/picard/picard_CollectAlignmentSummaryMetrics.xml @@ -15,24 +15,24 @@ @handle_reference_source@ picard CollectAlignmentSummaryMetrics - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -MAX_INSERT_SIZE ${maxinsert} + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --MAX_INSERT_SIZE ${maxinsert} #for $sequence in $adapters: - -ADAPTER_SEQUENCE '${sequence.adapter}' + --ADAPTER_SEQUENCE '${sequence.adapter}' #end for #for $level in str($metric_accumulation_level).split(','): - -METRIC_ACCUMULATION_LEVEL '${level}' + --METRIC_ACCUMULATION_LEVEL '${level}' #end for - -IS_BISULFITE_SEQUENCED '${bisulphite}' + --IS_BISULFITE_SEQUENCED '${bisulphite}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ASSUME_SORTED '${assume_sorted}' + --ASSUME_SORTED '${assume_sorted}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CollectBaseDistributionByCycle.xml b/tools/picard/picard_CollectBaseDistributionByCycle.xml index 8cac2ebbf17..a6d41d4a86c 100644 --- a/tools/picard/picard_CollectBaseDistributionByCycle.xml +++ b/tools/picard/picard_CollectBaseDistributionByCycle.xml @@ -16,17 +16,17 @@ @handle_reference_source@ picard CollectBaseDistributionByCycle - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -CHART_OUTPUT '${pdfFile}' - -ALIGNED_READS_ONLY '${aligned_reads_only}' - -PF_READS_ONLY '${pf_reads_only}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ASSUME_SORTED '${assume_sorted}' - - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --CHART_OUTPUT '${pdfFile}' + --ALIGNED_READS_ONLY '${aligned_reads_only}' + --PF_READS_ONLY '${pf_reads_only}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ASSUME_SORTED '${assume_sorted}' + + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CollectGcBiasMetrics.xml b/tools/picard/picard_CollectGcBiasMetrics.xml index cc904718bd8..932e31c1de8 100644 --- a/tools/picard/picard_CollectGcBiasMetrics.xml +++ b/tools/picard/picard_CollectGcBiasMetrics.xml @@ -16,19 +16,19 @@ @handle_reference_source@ picard CollectGcBiasMetrics - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -CHART_OUTPUT '${pdfFile}' - -SUMMARY_OUTPUT '${summaryFile}' - -WINDOW_SIZE '${window_size}' - -MINIMUM_GENOME_FRACTION '${minimum_genome_fraction}' - -IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ASSUME_SORTED '${assume_sorted}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --CHART_OUTPUT '${pdfFile}' + --SUMMARY_OUTPUT '${summaryFile}' + --WINDOW_SIZE '${window_size}' + --MINIMUM_GENOME_FRACTION '${minimum_genome_fraction}' + --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ASSUME_SORTED '${assume_sorted}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CollectHsMetrics.xml b/tools/picard/picard_CollectHsMetrics.xml index 3f6796b942f..6d922de2b14 100644 --- a/tools/picard/picard_CollectHsMetrics.xml +++ b/tools/picard/picard_CollectHsMetrics.xml @@ -9,17 +9,17 @@ @symlink_element_identifier@ picard CollectHsMetrics --INPUT '$escaped_element_identifier' --OUTPUT '${outFile}' --MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality} --MINIMUM_BASE_QUALITY ${minimum_base_quality} --COVERAGE_CAP ${coverage_cap} --CLIP_OVERLAPPING_READS ${clip_overlapping_reads} --BAIT_INTERVALS '${baitFile}' --TARGET_INTERVALS '${targetFile}' --VALIDATION_STRINGENCY ${validation_stringency} --QUIET true --VERBOSITY ERROR +--INPUT '$escaped_element_identifier' +--OUTPUT '${outFile}' +--MINIMUM_MAPPING_QUALITY ${minimum_mapping_quality} +--MINIMUM_BASE_QUALITY ${minimum_base_quality} +--COVERAGE_CAP ${coverage_cap} +--CLIP_OVERLAPPING_READS ${clip_overlapping_reads} +--BAIT_INTERVALS '${baitFile}' +--TARGET_INTERVALS '${targetFile}' +--VALIDATION_STRINGENCY ${validation_stringency} +--QUIET true +--VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CollectInsertSizeMetrics.xml b/tools/picard/picard_CollectInsertSizeMetrics.xml index 76e2d96db3b..2ec1a5b1a89 100644 --- a/tools/picard/picard_CollectInsertSizeMetrics.xml +++ b/tools/picard/picard_CollectInsertSizeMetrics.xml @@ -16,23 +16,23 @@ @handle_reference_source@ picard CollectInsertSizeMetrics - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -Histogram_FILE '${histFile}' - -DEVIATIONS '${deviations}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --Histogram_FILE '${histFile}' + --DEVIATIONS '${deviations}' #if str( $hist_width ): - -HISTOGRAM_WIDTH '${hist_width}' + --HISTOGRAM_WIDTH '${hist_width}' #end if - -MINIMUM_PCT '${min_pct}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ASSUME_SORTED '${assume_sorted}' - -METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}' + --MINIMUM_PCT '${min_pct}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ASSUME_SORTED '${assume_sorted}' + --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_CollectRnaSeqMetrics.xml b/tools/picard/picard_CollectRnaSeqMetrics.xml index 862ec6b7b3d..cac06fde018 100644 --- a/tools/picard/picard_CollectRnaSeqMetrics.xml +++ b/tools/picard/picard_CollectRnaSeqMetrics.xml @@ -35,27 +35,27 @@ @java_options@ picard CollectRnaSeqMetrics - -REF_FLATref Flat.tab + --REF_FLAT refFlat.tab #if str( $ribosomal_intervals ) != "None": - -RIBOSOMAL_INTERVALS '${ribosomal_intervals}' + --RIBOSOMAL_INTERVALS '${ribosomal_intervals}' #end if - -STRAND_SPECIFICITY '${strand_specificity}' - -MINIMUM_LENGTH '${minimum_length}' - -CHART_OUTPUT '${pdfFile}' + --STRAND_SPECIFICITY '${strand_specificity}' + --MINIMUM_LENGTH '${minimum_length}' + --CHART_OUTPUT '${pdfFile}' #for $sequence_to_ignore in $ignore_list: - -IGNORE_SEQUENCE '${sequence_to_ignore.sequence}' + --IGNORE_SEQUENCE '${sequence_to_ignore.sequence}' #end for - -RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}' - -METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}' - -INPUT '$escaped_element_identifier' + --RRNA_FRAGMENT_PERCENTAGE '${rrna_fragment_percentage}' + --METRIC_ACCUMULATION_LEVEL '${metric_accumulation_level}' + --INPUT '$escaped_element_identifier' -OUTPUT '${outFile}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ASSUME_SORTED '${assume_sorted}' - -VALIDATION_STRINGENCY ${validation_stringency} + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ASSUME_SORTED '${assume_sorted}' + --VALIDATION_STRINGENCY ${validation_stringency} ]]> diff --git a/tools/picard/picard_CollectSequencingArtifactsMetrics.xml b/tools/picard/picard_CollectSequencingArtifactsMetrics.xml index 6c60e7d9eb2..efa0f2812ac 100644 --- a/tools/picard/picard_CollectSequencingArtifactsMetrics.xml +++ b/tools/picard/picard_CollectSequencingArtifactsMetrics.xml @@ -14,23 +14,23 @@ @handle_reference_source@ picard CollectSequencingArtifactMetrics - -I '$escaped_element_identifier' - -O 'OutPut' - -R '${reference_fasta_filename}' - -AS ${assume_sorted} - -CONTEXT_SIZE ${context_size} - -INCLUDE_DUPLICATES '${duplicates}' + --I '$escaped_element_identifier' + --O 'OutPut' + --R '${reference_fasta_filename}' + --AS ${assume_sorted} + --CONTEXT_SIZE ${context_size} + --INCLUDE_DUPLICATES '${duplicates}' #if $contexts_to_print - #for $context in str($contexts_to_print).split(','): - -CONTEXTS_TO_PRINT '${context}' - #end for; + #for $context in str($contexts_to_print).split(','): + --CONTEXTS_TO_PRINT '${context}' + #end for; #end if; - -MINIMUM_QUALITY_SCORE '${min_quality_score}' - -INCLUDE_UNPAIRED '${unpaired}' - -MAXIMUM_INSERT_SIZE '${max_size}' - -MINIMUM_INSERT_SIZE '${min_size}' - -MINIMUM_MAPPING_QUALITY '${minim_map_quality}' - -VALIDATION_STRINGENCY '${validation_stringency}'; + --MINIMUM_QUALITY_SCORE '${min_quality_score}' + --INCLUDE_UNPAIRED '${unpaired}' + --MAXIMUM_INSERT_SIZE '${max_size}' + --MINIMUM_INSERT_SIZE '${min_size}' + --MINIMUM_MAPPING_QUALITY '${minim_map_quality}' + --VALIDATION_STRINGENCY '${validation_stringency}'; ]]> diff --git a/tools/picard/picard_CollectWgsMetrics.xml b/tools/picard/picard_CollectWgsMetrics.xml index 9b88698268c..05c78bd62ac 100644 --- a/tools/picard/picard_CollectWgsMetrics.xml +++ b/tools/picard/picard_CollectWgsMetrics.xml @@ -16,16 +16,16 @@ picard CollectWgsMetrics - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}' - -MINIMUM_BASE_QUALITY '${minimum_base_quality}' - -COVERAGE_CAP '${coverage_cap}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}' + --MINIMUM_BASE_QUALITY '${minimum_base_quality}' + --COVERAGE_CAP '${coverage_cap}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_DownsampleSam.xml b/tools/picard/picard_DownsampleSam.xml index 2d0dab4c44c..a35bb9bac8a 100644 --- a/tools/picard/picard_DownsampleSam.xml +++ b/tools/picard/picard_DownsampleSam.xml @@ -10,13 +10,13 @@ @symlink_element_identifier@ picard DownsampleSam - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -PROBABILITY ${probability} - -RANDOM_SEED ${seed} - -QUIET true - -VERBOSITY ERROR - -VALIDATION_STRINGENCY ${validation_stringency} + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --PROBABILITY ${probability} + --RANDOM_SEED ${seed} + --QUIET true + --VERBOSITY ERROR + --VALIDATION_STRINGENCY ${validation_stringency} ]]> diff --git a/tools/picard/picard_EstimateLibraryComplexity.xml b/tools/picard/picard_EstimateLibraryComplexity.xml index d8cc7c394b9..f02e9bd7292 100644 --- a/tools/picard/picard_EstimateLibraryComplexity.xml +++ b/tools/picard/picard_EstimateLibraryComplexity.xml @@ -11,19 +11,19 @@ picard EstimateLibraryComplexity - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - - -MIN_IDENTICAL_BASES '${min_identical_bases}' - -MAX_DIFF_RATE '${max_diff_rate}' - -MIN_MEAN_QUALITY '${min_mean_quality}' - -MAX_GROUP_RATIO '${max_group_ratio}' - -READ_NAME_REGEX '${ str( $read_name_regex ) }' - -OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' - - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + + --MIN_IDENTICAL_BASES '${min_identical_bases}' + --MAX_DIFF_RATE '${max_diff_rate}' + --MIN_MEAN_QUALITY '${min_mean_quality}' + --MAX_GROUP_RATIO '${max_group_ratio}' + --READ_NAME_REGEX '${ str( $read_name_regex ) }' + --OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' + + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_FastqToSam.xml b/tools/picard/picard_FastqToSam.xml index 4e43fbd3c26..892493a852f 100644 --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -2,7 +2,7 @@ convert Fastq data into unaligned BAM picard_macros.xml - 1 + 0 picard_fastqtosam @@ -24,75 +24,75 @@ #if $fwd.ext.endswith(".gz") gunzip -c '$fwd' > fwd.fastq && #else - ln -s '$fwd' fwd.fastq && + ln -sf '$fwd' fwd.fastq && #end if #if rev #if rev.ext.endswith(".gz") gunzip -c '$rev' > rev.fastq && #else - ln -s '$rev' rev.fastq && + ln -sf '$rev' rev.fastq && #end if #end if picard FastqToSam - -FASTQ fwd.fastq + --FASTQ fwd.fastq #if rev - -FASTQ2 rev.fastq + --FASTQ2 rev.fastq #end if #if $fwd.ext.startswith("fastqillumina") - -QUALITY_FORMAT "Illumina" + --QUALITY_FORMAT "Illumina" #else if $fwd.ext.startswith("fastqsolexa") - -QUALITY_FORMAT "Solexa" + --QUALITY_FORMAT "Solexa" #else - -QUALITY_FORMAT "Standard" + --QUALITY_FORMAT "Standard" #end if - -OUTPUT '${outFile}' - -READ_GROUP_NAME '${read_group_name}' - -SAMPLE_NAME '${sample_name}' + --OUTPUT '${outFile}' + --READ_GROUP_NAME '${read_group_name}' + --SAMPLE_NAME '${sample_name}' #if str( $library_name ): - -LIBRARY_NAME '${library_name}' + --LIBRARY_NAME '${library_name}' #end if #if str( $platform_unit ): - -PLATFORM_UNIT '${platform_unit}' + --PLATFORM_UNIT '${platform_unit}' #end if #if str( $platform ): - -PLATFORM '${platform}' + --PLATFORM '${platform}' #end if #if str( $sequencing_center ): - -SEQUENCING_CENTER '${sequencing_center}' + --SEQUENCING_CENTER '${sequencing_center}' #end if #if str( $predicted_insert_size ): - -PREDICTED_INSERT_SIZE '${predicted_insert_size}' + --PREDICTED_INSERT_SIZE '${predicted_insert_size}' #end if #if str( $comment ): - -COMMENT '${comment}' + --COMMENT '${comment}' #end if #if str( $description ): - -DESCRIPTION '${description}' + --DESCRIPTION '${description}' #end if #if str( $run_date ): - -RUN_DATE '${run_date}' + --RUN_DATE '${run_date}' #end if - -MIN_Q '${min_q}' - -MAX_Q '${max_q}' - -STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}' - -ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}' + --MIN_Q '${min_q}' + --MAX_Q '${max_q}' + --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}' + --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}' - -SORT_ORDER coordinate - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_FilterSamReads.xml b/tools/picard/picard_FilterSamReads.xml index 06704230b96..c272719514b 100644 --- a/tools/picard/picard_FilterSamReads.xml +++ b/tools/picard/picard_FilterSamReads.xml @@ -11,28 +11,28 @@ ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order picard SortSam - -INPUT '$escaped_element_identifier' - -OUTPUT query_sorted_bam.bam - -SORT_ORDER queryname - -VALIDATION_STRINGENCY LENIENT - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + --OUTPUT query_sorted_bam.bam + --SORT_ORDER queryname + --VALIDATION_STRINGENCY LENIENT + --QUIET true + --VERBOSITY ERROR && picard FilterSamReads - -INPUT query_sorted_bam.bam - -FILTER '${filter_type.filter}' + --INPUT query_sorted_bam.bam + --FILTER '${filter_type.filter}' #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): - -READ_LIST_FILE '${filter_type.read_list_file}' + --READ_LIST_FILE '${filter_type.read_list_file}' #end if - -OUTPUT '${outFile}' - -SORT_ORDER coordinate - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --OUTPUT '${outFile}' + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_FixMateInformation.xml b/tools/picard/picard_FixMateInformation.xml index ebda5764229..33874768d6f 100644 --- a/tools/picard/picard_FixMateInformation.xml +++ b/tools/picard/picard_FixMateInformation.xml @@ -8,15 +8,15 @@ diff --git a/tools/picard/picard_MarkDuplicates.xml b/tools/picard/picard_MarkDuplicates.xml index 8a3b3f12f7b..18924b4fbef 100644 --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -10,32 +10,32 @@ @symlink_element_identifier@ picard MarkDuplicates - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' - -METRICS_FILE '${metrics_file}' + --METRICS_FILE '${metrics_file}' #for $element in $comments: - -COMMENT '${element.comment}' + --COMMENT '${element.comment}' #end for - -REMOVE_DUPLICATES '${remove_duplicates}' - -ASSUME_SORTED '${assume_sorted}' + --REMOVE_DUPLICATES '${remove_duplicates}' + --ASSUME_SORTED '${assume_sorted}' - -DUPLICATE_SCORING_STRATEGY '${duplicate_scoring_strategy}' + --DUPLICATE_SCORING_STRATEGY ${duplicate_scoring_strategy} #if $read_name_regex: - -READ_NAME_REGEX '${ str( $read_name_regex ) }' + --READ_NAME_REGEX '${ str( $read_name_regex ) }' #end if - -OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' + --OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' #if $barcode_tag: - -BARCODE_TAG '${barcode_tag}' + --BARCODE_TAG '${barcode_tag}' #end if - -VALIDATION_STRINGENCY '${validation_stringency}' - -TAGGING_POLICY All - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --TAGGING_POLICY All + --QUIET true + --VERBOSITY ERROR ]]> @@ -46,8 +46,9 @@ - + + diff --git a/tools/picard/picard_MarkDuplicatesWithMateCigar.xml b/tools/picard/picard_MarkDuplicatesWithMateCigar.xml index 01925a6b26d..611c66459b3 100644 --- a/tools/picard/picard_MarkDuplicatesWithMateCigar.xml +++ b/tools/picard/picard_MarkDuplicatesWithMateCigar.xml @@ -10,27 +10,27 @@ @symlink_element_identifier@ picard MarkDuplicatesWithMateCigar - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' - -METRICS_FILE '${metrics_file}' - -COMMENT '${comment}' + --METRICS_FILE '${metrics_file}' + --COMMENT '${comment}' - -MINIMUM_DISTANCE '${minimum_distance}' - -SKIP_PAIRS_WITH_NO_MATE_CIGAR '${skip_pairs_with_no_mate_cigar}' + --MINIMUM_DISTANCE '${minimum_distance}' + --SKIP_PAIRS_WITH_NO_MATE_CIGAR '${skip_pairs_with_no_mate_cigar}' - -REMOVE_DUPLICATES '${remove_duplicates}' - -ASSUME_SORTED '${assume_sorted}' + --REMOVE_DUPLICATES '${remove_duplicates}' + --ASSUME_SORTED '${assume_sorted}' - -DUPLICATE_SCORING_STRATEGY '${duplicate_scoring_strategy}' + --DUPLICATE_SCORING_STRATEGY ${duplicate_scoring_strategy} - -READ_NAME_REGEX '${ str( $read_name_regex ) }' - -OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' + --READ_NAME_REGEX '${ str( $read_name_regex ) }' + --OPTICAL_DUPLICATE_PIXEL_DISTANCE '${optical_duplicate_pixel_distance}' - -BLOCK_SIZE 100000 - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --BLOCK_SIZE 100000 + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> @@ -43,6 +43,7 @@ + diff --git a/tools/picard/picard_MeanQualityByCycle.xml b/tools/picard/picard_MeanQualityByCycle.xml index 08ae8619f2f..77b5ef90b9f 100644 --- a/tools/picard/picard_MeanQualityByCycle.xml +++ b/tools/picard/picard_MeanQualityByCycle.xml @@ -15,18 +15,18 @@ @handle_reference_source@ picard MeanQualityByCycle - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -CHART_OUTPUT '${pdfFile}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ALIGNED_READS_ONLY '${aligned_reads_only}' - -PF_READS_ONLY '${pf_reads_only}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --CHART_OUTPUT '${pdfFile}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ALIGNED_READS_ONLY '${aligned_reads_only}' + --PF_READS_ONLY '${pf_reads_only}' - -ASSUME_SORTED '${assume_sorted}' + --ASSUME_SORTED '${assume_sorted}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_MergeBamAlignment.xml b/tools/picard/picard_MergeBamAlignment.xml index 388158b672a..ac144798e4c 100644 --- a/tools/picard/picard_MergeBamAlignment.xml +++ b/tools/picard/picard_MergeBamAlignment.xml @@ -29,63 +29,63 @@ #end if picard MergeBamAlignment - -UNMAPPED_BAM '${unmapped_bam}' + --UNMAPPED_BAM '${unmapped_bam}' - -PAIRED_RUN true ##This argument is ignored and will be removed. Required. Possible values: {true, false} + --PAIRED_RUN true ##This argument is ignored and will be removed. Required. Possible values: {true, false} #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file": #for $dataset in $aligned_or_read1_and_read2.aligned_bams: - -ALIGNED_BAM '${dataset.aligned_bam}' + --ALIGNED_BAM '${dataset.aligned_bam}' #end for #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files": #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: - -READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}' + --READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}' #end for #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams: - -READ2_ALIGNED_BAM '${dataset.read2_aligned_bam}' + --READ2_ALIGNED_BAM '${dataset.read2_aligned_bam}' #end for #else #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams: - -READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}' + --READ1_ALIGNED_BAM '${dataset.read1_aligned_bam}' #end for #end if - -OUTPUT '${outFile}' - -REFERENCE_SEQUENCE '${ref_fasta}' + --OUTPUT '${outFile}' + --REFERENCE_SEQUENCE '${ref_fasta}' - -CLIP_ADAPTERS '${clip_adapters}' - -IS_BISULFITE_SEQUENCE '${is_bisulfite_sequence}' - -ALIGNED_READS_ONLY '${aligned_reads_only}' - -MAX_INSERTIONS_OR_DELETIONS '${max_insertions_or_deletions}' + --CLIP_ADAPTERS '${clip_adapters}' + --IS_BISULFITE_SEQUENCE '${is_bisulfite_sequence}' + --ALIGNED_READS_ONLY '${aligned_reads_only}' + --MAX_INSERTIONS_OR_DELETIONS '${max_insertions_or_deletions}' #for $attribute in $attributes_to_retain: - -ATTRIBUTES_TO_RETAIN '${$attribute.attribute}' + --ATTRIBUTES_TO_RETAIN '${$attribute.attribute}' #end for #for $attribute in $attributes_to_remove: - -ATTRIBUTES_TO_REMOVE '${$attribute.attribute}' + --ATTRIBUTES_TO_REMOVE '${$attribute.attribute}' #end for - -READ1_TRIM '${read1_trim}' - -READ2_TRIM '${read2_trim}' + --READ1_TRIM '${read1_trim}' + --READ2_TRIM '${read2_trim}' #if str( $orientations ) != "None": #for $orientation in str( $orientations ).split(','): ## See trello card https://trello.com/c/9nW02Zhd - -EXPECTED_ORIENTATIONS '${orientation}' + --EXPECTED_ORIENTATIONS '${orientation}' #end for #end if - -ALIGNER_PROPER_PAIR_FLAGS '${aligner_proper_pair_flags}' - -PRIMARY_ALIGNMENT_STRATEGY '${primary_alignment_strategy}' - -CLIP_OVERLAPPING_READS '${clip_overlapping_reads}' - -INCLUDE_SECONDARY_ALIGNMENTS '${include_secondary_alignments}' - -ADD_MATE_CIGAR '${add_mate_cigar}' + --ALIGNER_PROPER_PAIR_FLAGS '${aligner_proper_pair_flags}' + --PRIMARY_ALIGNMENT_STRATEGY '${primary_alignment_strategy}' + --CLIP_OVERLAPPING_READS '${clip_overlapping_reads}' + --INCLUDE_SECONDARY_ALIGNMENTS '${include_secondary_alignments}' + --ADD_MATE_CIGAR '${add_mate_cigar}' - -VALIDATION_STRINGENCY '${validation_stringency}' + --VALIDATION_STRINGENCY '${validation_stringency}' - -SORT_ORDER coordinate - -QUIET true - -VERBOSITY ERROR + --SORT_ORDER coordinate + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_MergeSamFiles.xml b/tools/picard/picard_MergeSamFiles.xml index ed325ec8376..7d1af59aa2e 100644 --- a/tools/picard/picard_MergeSamFiles.xml +++ b/tools/picard/picard_MergeSamFiles.xml @@ -10,22 +10,22 @@ picard MergeSamFiles #for $element in $inputFile: - -INPUT '${element}' + --INPUT '${element}' #end for - -OUTPUT '${outFile}' - -MERGE_SEQUENCE_DICTIONARIES '${merge_sequence_dictionaries}' + --OUTPUT '${outFile}' + --MERGE_SEQUENCE_DICTIONARIES '${merge_sequence_dictionaries}' - -ASSUME_SORTED '${assume_sorted}' + --ASSUME_SORTED '${assume_sorted}' #for $element in $comments: - -COMMENT '${element.comment}' + --COMMENT '${element.comment}' #end for - -USE_THREADING true - -SORT_ORDER coordinate - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --USE_THREADING true + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_NormalizeFasta.xml b/tools/picard/picard_NormalizeFasta.xml index c0adb2b6fd1..8de70779d2a 100644 --- a/tools/picard/picard_NormalizeFasta.xml +++ b/tools/picard/picard_NormalizeFasta.xml @@ -15,13 +15,13 @@ picard NormalizeFasta - -INPUT '$escaped_element_identifier'.fa - -OUTPUT '${outFile}' - -LINE_LENGTH '${line_length}' - -TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}' + --INPUT '$escaped_element_identifier'.fa + --OUTPUT '${outFile}' + --LINE_LENGTH '${line_length}' + --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}' - -QUIET true - -VERBOSITY ERROR + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_QualityScoreDistribution.xml b/tools/picard/picard_QualityScoreDistribution.xml index 76725e04948..57471d2cc98 100644 --- a/tools/picard/picard_QualityScoreDistribution.xml +++ b/tools/picard/picard_QualityScoreDistribution.xml @@ -15,19 +15,19 @@ @handle_reference_source@ picard QualityScoreDistribution - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -CHART_OUTPUT '${pdfFile}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -ALIGNED_READS_ONLY '${aligned_reads_only}' - -PF_READS_ONLY '${pf_reads_only}' - -INCLUDE_NO_CALLS '${include_no_calls}' - - -ASSUME_SORTED '${assume_sorted}' - - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --CHART_OUTPUT '${pdfFile}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --ALIGNED_READS_ONLY '${aligned_reads_only}' + --PF_READS_ONLY '${pf_reads_only}' + --INCLUDE_NO_CALLS '${include_no_calls}' + + --ASSUME_SORTED '${assume_sorted}' + + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_ReorderSam.xml b/tools/picard/picard_ReorderSam.xml index 904f739405d..cd20986f3d4 100644 --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -18,9 +18,11 @@ #if str( $reference_source.reference_source_selector ) == "history": - picard CreateSequenceDictionary REFERENCE='${ref_fasta}' OUTPUT='${picard_dict}' - QUIET=true - VERBOSITY=ERROR + picard CreateSequenceDictionary + --REFERENCE='${ref_fasta}' + --OUTPUT='${picard_dict}' + --QUIET=true + --VERBOSITY=ERROR && @@ -32,15 +34,15 @@ picard ReorderSam - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -SEQUENCE_DICTIONARY '${ref_fasta}' - -ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}' - -ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}' - - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --SEQUENCE_DICTIONARY '${ref_fasta}' + --ALLOW_INCOMPLETE_DICT_CONCORDANCE '${allow_incomplete_dict_concordance}' + --ALLOW_CONTIG_LENGTH_DISCORDANCE '${allow_contig_length_discordance}' + + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_ReplaceSamHeader.xml b/tools/picard/picard_ReplaceSamHeader.xml index 9f418daaa1c..9bcdd0128e7 100644 --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -18,12 +18,12 @@ picard ReplaceSamHeader - -INPUT '$escaped_element_identifier' - -HEADER '${header}' - -OUTPUT '${outFile}' + --INPUT '$escaped_element_identifier' + --HEADER '${header}' + --OUTPUT '${outFile}' - -QUIET true - -VERBOSITY ERROR + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml b/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml index a4130233b1f..3c019d8df8d 100644 --- a/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml +++ b/tools/picard/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @@ -9,16 +9,16 @@ @java_options@ picard RevertOriginalBaseQualitiesAndAddMateCigar - -INPUT '$inputFile' - -OUTPUT '${outFile}' + --INPUT '$inputFile' + --OUTPUT '${outFile}' - -RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}' - -MAX_RECORDS_TO_EXAMINE '${max_records_to_examine}' + --RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}' + --MAX_RECORDS_TO_EXAMINE '${max_records_to_examine}' - -SORT_ORDER coordinate - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --SORT_ORDER coordinate + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_RevertSam.xml b/tools/picard/picard_RevertSam.xml index 213bd811813..838bf0b7722 100644 --- a/tools/picard/picard_RevertSam.xml +++ b/tools/picard/picard_RevertSam.xml @@ -9,26 +9,26 @@ @java_options@ picard RevertSam - -INPUT '$inputFile' - -OUTPUT '${outFile}' + --INPUT '$inputFile' + --OUTPUT '${outFile}' - -RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}' - -REMOVE_DUPLICATE_INFORMATION '${remove_duplicate_information}' - -REMOVE_ALIGNMENT_INFORMATION '${remove_alignment_information}' + --RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}' + --REMOVE_DUPLICATE_INFORMATION '${remove_duplicate_information}' + --REMOVE_ALIGNMENT_INFORMATION '${remove_alignment_information}' #for $attribute_to_clear in $attributes_to_clear: - -ATTRIBUTE_TO_CLEAR '${attribute_to_clear.attribute}' + --ATTRIBUTE_TO_CLEAR '${attribute_to_clear.attribute}' #end for - -SANITIZE '${sanitize}' - -MAX_DISCARD_FRACTION '${max_discard_fraction}' - -SAMPLE_ALIAS '${sample_alias}' - -LIBRARY_NAME '${library_name}' + --SANITIZE '${sanitize}' + --MAX_DISCARD_FRACTION '${max_discard_fraction}' + --SAMPLE_ALIAS '${sample_alias}' + --LIBRARY_NAME '${library_name}' - -SORT_ORDER '${sort_order}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --SORT_ORDER '${sort_order}' + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_SamToFastq.xml b/tools/picard/picard_SamToFastq.xml index c683e8c3b06..0b45f7b6803 100644 --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -15,45 +15,45 @@ picard SamToFastq - -INPUT '$escaped_element_identifier' + --INPUT '$escaped_element_identifier' #if str($single_or_paired) == "pe_interleaved": - -FASTQ '${interleaved_fastq}' - -INTERLEAVE TRUE + --FASTQ '${interleaved_fastq}' + --INTERLEAVE TRUE #else if str($single_or_paired) == "pe_sep": - -F '${fq1}' - -F2 '${fq2}' - -FU '${fq_u}' + --F '${fq1}' + --F2 '${fq2}' + --FU '${fq_u}' #else - -F '${fq_single}' + --F '${fq_single}' #end if - -RE_REVERSE '${re_reverse}' + --RE_REVERSE '${re_reverse}' -INCLUDE_NON_PF_READS '${include_non_pf_reads}' #if len(str($clipping_attribute)) > 0: - -CLIPPING_ATTRIBUTE '${clipping_attribute}' + --CLIPPING_ATTRIBUTE '${clipping_attribute}' #end if #if len(str($clipping_action)) > 0: - -CLIPPING_ACTION '${clipping_action}' + --CLIPPING_ACTION '${clipping_action}' #end if - -READ1_TRIM '${read1_trim}' + --READ1_TRIM '${read1_trim}' #if int($read1_max_bases_to_write) > -1: - -READ1_MAX_BASES_TO_WRITE '${read1_max_bases_to_write}' + --READ1_MAX_BASES_TO_WRITE '${read1_max_bases_to_write}' #end if - -READ2_TRIM '${read2_trim}' + --READ2_TRIM '${read2_trim}' #if int($read2_max_bases_to_write) > -1: - -READ2_MAX_BASES_TO_WRITE '${read2_max_bases_to_write}' + --READ2_MAX_BASES_TO_WRITE '${read2_max_bases_to_write}' #end if - -INCLUDE_NON_PRIMARY_ALIGNMENTS '${include_non_primary_alignments}' + --INCLUDE_NON_PRIMARY_ALIGNMENTS '${include_non_primary_alignments}' - -VALIDATION_STRINGENCY '${validation_stringency}' - -QUIET true - -VERBOSITY ERROR + --VALIDATION_STRINGENCY '${validation_stringency}' + --QUIET true + --VERBOSITY ERROR ]]> diff --git a/tools/picard/picard_SortSam.xml b/tools/picard/picard_SortSam.xml index 82e2b08b82e..c545bdfa5b1 100644 --- a/tools/picard/picard_SortSam.xml +++ b/tools/picard/picard_SortSam.xml @@ -15,12 +15,12 @@ @java_options@ @symlink_element_identifier@ picard SortSam - -INPUT '$escaped_element_identifier' - -OUTPUT '${output}' - -SORT_ORDER '${sort_order}' - -QUIET true - -VERBOSITY ERROR - -VALIDATION_STRINGENCY ${validation_stringency} + --INPUT '$escaped_element_identifier' + --OUTPUT '${output}' + --SORT_ORDER '${sort_order}' + --QUIET true + --VERBOSITY ERROR + --VALIDATION_STRINGENCY ${validation_stringency} ]]> diff --git a/tools/picard/picard_ValidateSamFile.xml b/tools/picard/picard_ValidateSamFile.xml index 79e71583bea..efe780138d7 100644 --- a/tools/picard/picard_ValidateSamFile.xml +++ b/tools/picard/picard_ValidateSamFile.xml @@ -30,24 +30,24 @@ picard ValidateSamFile - -INPUT '$escaped_element_identifier' - -OUTPUT '${outFile}' - -MODE '${mode}' + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --MODE '${mode}' #if str( $ignore ) != "None": #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd - -IGNORE '${element}' + --IGNORE '${element}' #end for #end if - -MAX_OUTPUT '${max_output}' - -REFERENCE_SEQUENCE '${reference_fasta_filename}' - -IGNORE_WARNINGS '${ignore_warnings}' - -IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' - -MAX_OPEN_TEMP_FILES `ulimit -Sn` + --MAX_OUTPUT '${max_output}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --IGNORE_WARNINGS '${ignore_warnings}' + --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' + --MAX_OPEN_TEMP_FILES `ulimit -Sn` - -VERBOSITY ERROR - -QUIET true + --VERBOSITY ERROR + --QUIET true ]]>