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oh Picard ...
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@bgruening
bgruening committed Mar 2, 2024
1 parent 849d153 commit d462e02
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Showing 31 changed files with 364 additions and 360 deletions.
12 changes: 6 additions & 6 deletions tools/picard/picard_AddCommentsToBam.xml
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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 ${validation_stringency}
]]></command>
<inputs>
<param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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26 changes: 13 additions & 13 deletions tools/picard/picard_AddOrReplaceReadGroups.xml
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@java_options@
@symlink_element_identifier@
picard AddOrReplaceReadGroups
-INPUT '$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 '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
]]></command>
<inputs>
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10 changes: 5 additions & 5 deletions tools/picard/picard_BedToIntervalList.xml
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picard
BedToIntervalList
-INPUT '$escaped_element_identifier'
-OUTPUT '${outFile}'
--INPUT '$escaped_element_identifier'
--OUTPUT '${outFile}'
-SEQUENCE_DICTIONARY '${picard_dict}'
-QUIET true
-VERBOSITY ERROR
--SEQUENCE_DICTIONARY '${picard_dict}'
--QUIET true
--VERBOSITY ERROR
]]></command>
<inputs>
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10 changes: 5 additions & 5 deletions tools/picard/picard_CleanSam.xml
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@java_options@
@symlink_element_identifier@
picard CleanSam
-INPUT '$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 ${validation_stringency}
]]></command>
<inputs>
<param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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22 changes: 11 additions & 11 deletions tools/picard/picard_CollectAlignmentSummaryMetrics.xml
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@handle_reference_source@
picard CollectAlignmentSummaryMetrics
-INPUT '$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
]]></command>
<inputs>
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22 changes: 11 additions & 11 deletions tools/picard/picard_CollectBaseDistributionByCycle.xml
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@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
]]></command>
<inputs>
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24 changes: 12 additions & 12 deletions tools/picard/picard_CollectGcBiasMetrics.xml
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@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
]]></command>
<inputs>
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22 changes: 11 additions & 11 deletions tools/picard/picard_CollectHsMetrics.xml
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Expand Up @@ -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 ${validation_stringency}
--QUIET true
--VERBOSITY ERROR
]]></command>
<inputs>
<param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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24 changes: 12 additions & 12 deletions tools/picard/picard_CollectInsertSizeMetrics.xml
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Expand Up @@ -16,23 +16,23 @@
@handle_reference_source@
picard CollectInsertSizeMetrics
-INPUT '$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
]]></command>
<inputs>
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24 changes: 12 additions & 12 deletions tools/picard/picard_CollectRnaSeqMetrics.xml
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Expand Up @@ -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 ${validation_stringency}
]]></command>
<inputs>
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30 changes: 15 additions & 15 deletions tools/picard/picard_CollectSequencingArtifactsMetrics.xml
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Expand Up @@ -14,23 +14,23 @@
@handle_reference_source@
picard CollectSequencingArtifactMetrics
-I '$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 '${validation_stringency}';
]]></command>
<inputs>
<param name="inputFile" format="sam,bam" type="data" label="SAM/BAM Input file"/>
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18 changes: 9 additions & 9 deletions tools/picard/picard_CollectWgsMetrics.xml
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Expand Up @@ -16,16 +16,16 @@
picard
CollectWgsMetrics
-INPUT '$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 '${validation_stringency}'
--QUIET true
--VERBOSITY ERROR
]]></command>
<inputs>
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14 changes: 7 additions & 7 deletions tools/picard/picard_DownsampleSam.xml
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Expand Up @@ -10,13 +10,13 @@
@symlink_element_identifier@
picard
DownsampleSam
-INPUT '$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}
]]></command>
<inputs>
<param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset"/>
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