Lint and tests

galaxyproject · Sep 1, 2023 · b059603 · b059603
1 parent ba9b83e
commit b059603
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Showing 36 changed files with 574 additions and 408 deletions.
diff --git a/macros/read_group_macros.xml b/macros/read_group_macros.xml
@@ -138,9 +138,11 @@
 #set $use_rg = str($rg.rg_selector) != "do_not_set"
     </token>
     <xml name="read_group_auto_name_conditional">
-        <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" />
-        <when value="true">
-        </when>
+        <param name="do_auto_name" type="select" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value">
+            <option value="false">False</option>
+            <option value="true">True</option>
+        </param>
+        <when value="true"/>
         <when value="false">
             <yield />
         </when>

diff --git a/tools/picard/picard_AddCommentsToBam.xml b/tools/picard/picard_AddCommentsToBam.xml
@@ -9,15 +9,15 @@
     @symlink_element_identifier@
     picard
       AddCommentsToBam
-      INPUT='$escaped_element_identifier'
-      OUTPUT="${outFile}"
+      -INPUT='$escaped_element_identifier'
+      -OUTPUT="${outFile}"
       #for $element in $comments:
-        COMMENT="${element.comment}"
+        -COMMENT="${element.comment}"
       #end for
-      QUIET=true
-      VERBOSITY=ERROR
+      -QUIET=true
+      -VERBOSITY=ERROR
       @TMPDIR_OPTION@
-      VALIDATION_STRINGENCY=${validation_stringency}
+      -VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
 
   <inputs>

diff --git a/tools/picard/picard_AddOrReplaceReadGroups.xml b/tools/picard/picard_AddOrReplaceReadGroups.xml
@@ -13,7 +13,7 @@
     @symlink_element_identifier@
     picard
       AddOrReplaceReadGroups
-      INPUT='$escaped_element_identifier'
+      -INPUT='$escaped_element_identifier'
       $format_read_group("RGLB=", $rg_lb, '"')
       $format_read_group("RGPL=", $rg_pl, '"')
       $format_read_group("RGPU=", $rg_pu, '"')
@@ -22,11 +22,11 @@
       $format_read_group("RGDS=", $rg_ds, '"')
       $format_read_group("RGPI=", $rg_pi, '"')
       $format_read_group("RGDT=", $rg_dt, '"')
-      VALIDATION_STRINGENCY="${validation_stringency}"
-      QUIET=true
-      VERBOSITY=ERROR
+      -VALIDATION_STRINGENCY="${validation_stringency}"
+      -QUIET=true
+      -VERBOSITY=ERROR
       @TMPDIR_OPTION@
-      OUTPUT="${outFile}"
+      -OUTPUT="${outFile}"
 
   ]]></command>
 

diff --git a/tools/picard/picard_BedToIntervalList.xml b/tools/picard/picard_BedToIntervalList.xml
@@ -14,10 +14,13 @@
 
     #if str( $reference_source.reference_source_selector ) == "history":
 
-      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
-      QUIET=true
-      VERBOSITY=ERROR
-      @TMPDIR_OPTION@
+      picard 
+        CreateSequenceDictionary 
+        -REFERENCE="${ref_fasta}" 
+        -OUTPUT="${picard_dict}"
+        -QUIET=true
+        -VERBOSITY=ERROR
+        @TMPDIR_OPTION@
 
       &&
 
@@ -30,12 +33,12 @@
 
     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
       @TMPDIR_OPTION@
 
   ]]></command>

diff --git a/tools/picard/picard_CleanSam.xml b/tools/picard/picard_CleanSam.xml
@@ -9,12 +9,12 @@
     @symlink_element_identifier@
     picard
     CleanSam
-    INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
-    QUIET=true
-    VERBOSITY=ERROR
+    -INPUT='$escaped_element_identifier'
+    -OUTPUT="${outFile}"
+    -QUIET=true
+    -VERBOSITY=ERROR
     @TMPDIR_OPTION@
-    VALIDATION_STRINGENCY=${validation_stringency}
+    -VALIDATION_STRINGENCY=${validation_stringency}
   ]]></command>
 
   <inputs>

diff --git a/tools/picard/picard_CollectAlignmentSummaryMetrics.xml b/tools/picard/picard_CollectAlignmentSummaryMetrics.xml
@@ -15,24 +15,24 @@
 
     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
     @TMPDIR_OPTION@
 
   ]]></command>

diff --git a/tools/picard/picard_CollectBaseDistributionByCycle.xml b/tools/picard/picard_CollectBaseDistributionByCycle.xml
@@ -4,7 +4,7 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="@R_BASE_VERSION@">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
@@ -17,17 +17,17 @@
 
     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
     @TMPDIR_OPTION@
 
   ]]></command>

diff --git a/tools/picard/picard_CollectGcBiasMetrics.xml b/tools/picard/picard_CollectGcBiasMetrics.xml
@@ -4,7 +4,7 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="@R_BASE_VERSION@">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
@@ -17,19 +17,19 @@
 
     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="${assume_sorted}"
-
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
+    -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
     @TMPDIR_OPTION@
 
   ]]></command>

diff --git a/tools/picard/picard_CollectHsMetrics.xml b/tools/picard/picard_CollectHsMetrics.xml
@@ -10,17 +10,17 @@
 
 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
 @TMPDIR_OPTION@
     ]]></command>
     <inputs>

diff --git a/tools/picard/picard_CollectInsertSizeMetrics.xml b/tools/picard/picard_CollectInsertSizeMetrics.xml
@@ -4,7 +4,7 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="@R_BASE_VERSION@">r-base</requirement>
+    <requirement type="package" version="4.3.0">r-base</requirement>
   </expand>
   <command detect_errors="exit_code"><![CDATA[
     @java_options@
@@ -17,23 +17,23 @@
 
     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
     @TMPDIR_OPTION@
 
   ]]></command>

diff --git a/tools/picard/picard_CollectRnaSeqMetrics.xml b/tools/picard/picard_CollectRnaSeqMetrics.xml
@@ -4,7 +4,7 @@
         <import>picard_macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="@R_BASE_VERSION@">r-base</requirement>
+        <requirement type="package" version="4.3.0">r-base</requirement>
         <requirement type="package" version="377">ucsc-gff3togenepred</requirement>
         <requirement type="package" version="377">ucsc-gtftogenepred</requirement>
     </expand>
@@ -36,28 +36,28 @@
       @java_options@
       picard
       CollectRnaSeqMetrics
-      REF_FLAT=refFlat.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='$escaped_element_identifier'
-      OUTPUT="${outFile}"
-      REFERENCE_SEQUENCE="${reference_fasta_filename}"
-      ASSUME_SORTED="${assume_sorted}"
+      -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}"
       @TMPDIR_OPTION@
-      VALIDATION_STRINGENCY=${validation_stringency}
+      -VALIDATION_STRINGENCY=${validation_stringency}
 
    ]]></command>