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changeset 9:41b8d087a2d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
author devteam
date Wed, 07 Dec 2016 14:56:16 -0500
parents e417b1d6288d
children 126c30841c38
files picard_AddCommentsToBam.xml picard_AddOrReplaceReadGroups.xml picard_BedToIntervalList.xml picard_CleanSam.xml picard_CollectAlignmentSummaryMetrics.xml picard_CollectBaseDistributionByCycle.xml picard_CollectGcBiasMetrics.xml picard_CollectInsertSizeMetrics.xml picard_CollectRnaSeqMetrics.xml picard_CollectWgsMetrics.xml picard_DownsampleSam.xml picard_EstimateLibraryComplexity.xml picard_FilterSamReads.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_MeanQualityByCycle.xml picard_NormalizeFasta.xml picard_QualityScoreDistribution.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml picard_SortSam.xml picard_ValidateSamFile.xml picard_macros.xml
diffstat 24 files changed, 29 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/picard_AddCommentsToBam.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_AddCommentsToBam.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -9,7 +9,7 @@
     @symlink_element_identifier@
     picard
       AddCommentsToBam
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
       #for $element in $comments:
         COMMENT="${element.comment}"
--- a/picard_AddOrReplaceReadGroups.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_AddOrReplaceReadGroups.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -13,7 +13,7 @@
     @symlink_element_identifier@
     picard
       AddOrReplaceReadGroups
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       $format_read_group("RGLB=", $rg_lb, '"')
       $format_read_group("RGPL=", $rg_pl, '"')
       $format_read_group("RGPU=", $rg_pu, '"')
--- a/picard_BedToIntervalList.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_BedToIntervalList.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -29,7 +29,7 @@
 
     picard
       BedToIntervalList
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
 
       SEQUENCE_DICTIONARY="${picard_dict}"
--- a/picard_CleanSam.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CleanSam.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -9,7 +9,7 @@
     @symlink_element_identifier@
     picard
     CleanSam
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     QUIET=true
     VERBOSITY=ERROR
--- a/picard_CollectAlignmentSummaryMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -19,7 +19,7 @@
 
     picard
     CollectAlignmentSummaryMetrics
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     MAX_INSERT_SIZE=${maxinsert}
     #for $sequence in $adapters:
--- a/picard_CollectBaseDistributionByCycle.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectBaseDistributionByCycle.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -21,7 +21,7 @@
 
     picard
     CollectBaseDistributionByCycle
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     ALIGNED_READS_ONLY="${aligned_reads_only}"
--- a/picard_CollectGcBiasMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectGcBiasMetrics.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -21,7 +21,7 @@
 
     picard
     CollectGcBiasMetrics
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     SUMMARY_OUTPUT="${summaryFile}"
--- a/picard_CollectInsertSizeMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectInsertSizeMetrics.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -21,7 +21,7 @@
 
     picard
     CollectInsertSizeMetrics
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     HISTOGRAM_FILE="${histFile}"
     DEVIATIONS="${deviations}"
--- a/picard_CollectRnaSeqMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectRnaSeqMetrics.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -46,7 +46,7 @@
 
       RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"
       METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
       REFERENCE_SEQUENCE="${reference_fasta_filename}"
       ASSUME_SORTED="${assume_sorted}"
--- a/picard_CollectWgsMetrics.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_CollectWgsMetrics.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -19,7 +19,7 @@
 
     picard
     CollectWgsMetrics
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
--- a/picard_DownsampleSam.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_DownsampleSam.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -9,7 +9,7 @@
     @symlink_element_identifier@
     picard
     DownsampleSam
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
       PROBABILITY=${probability}
       RANDOM_SEED=${seed}
--- a/picard_EstimateLibraryComplexity.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_EstimateLibraryComplexity.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -10,7 +10,7 @@
     picard
     EstimateLibraryComplexity
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
 
     MIN_IDENTICAL_BASES="${min_identical_bases}"
--- a/picard_FilterSamReads.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_FilterSamReads.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -11,7 +11,7 @@
 
     picard
     SortSam
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT=query_sorted_bam.bam
     SORT_ORDER=queryname
     VALIDATION_STRINGENCY=LENIENT
--- a/picard_MarkDuplicates.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_MarkDuplicates.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -10,7 +10,7 @@
     picard
     MarkDuplicates
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
 
     METRICS_FILE="${metrics_file}"
--- a/picard_MarkDuplicatesWithMateCigar.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_MarkDuplicatesWithMateCigar.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -10,7 +10,7 @@
     picard
     MarkDuplicatesWithMateCigar
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
 
     METRICS_FILE="${metrics_file}"
--- a/picard_MeanQualityByCycle.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_MeanQualityByCycle.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -20,7 +20,7 @@
 
     picard
     MeanQualityByCycle
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
--- a/picard_NormalizeFasta.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_NormalizeFasta.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -8,12 +8,13 @@
     @java_options@
 
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
-    ln -s '$inputFile' '$inputFile.element_identifier'.fa &&
-
+    #import re
+    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
+    ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
     picard
     NormalizeFasta
 
-    INPUT='$inputFile.element_identifier'.fa
+    INPUT='$escaped_element_identifier'.fa
     OUTPUT="${outFile}"
     LINE_LENGTH="${line_length}"
     TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"
--- a/picard_QualityScoreDistribution.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_QualityScoreDistribution.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -20,7 +20,7 @@
 
     picard
     QualityScoreDistribution
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     CHART_OUTPUT="${pdfFile}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
--- a/picard_ReorderSam.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_ReorderSam.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -28,7 +28,7 @@
 
     picard
     ReorderSam
-      INPUT='$inputFile.element_identifier'
+      INPUT='$escaped_element_identifier'
       OUTPUT="${outFile}"
       REFERENCE="${ref_fasta}"
       ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
--- a/picard_ReplaceSamHeader.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_ReplaceSamHeader.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -15,7 +15,7 @@
     picard
     ReplaceSamHeader
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     HEADER="${header}"
     OUTPUT="${outFile}"
 
--- a/picard_SamToFastq.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_SamToFastq.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -14,7 +14,7 @@
     picard
     SamToFastq
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
 
     #if str( $output_per_rg ) == "true":
       OUTPUT_PER_RG=true
--- a/picard_SortSam.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_SortSam.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -15,7 +15,7 @@
     @symlink_element_identifier@
     picard
     SortSam
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT='${output}'
     SORT_ORDER="${sort_order}"
     QUIET=true
--- a/picard_ValidateSamFile.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_ValidateSamFile.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -30,7 +30,7 @@
     picard
     ValidateSamFile
 
-    INPUT='$inputFile.element_identifier'
+    INPUT='$escaped_element_identifier'
     OUTPUT="${outFile}"
     MODE="${mode}"
 
--- a/picard_macros.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_macros.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -17,7 +17,9 @@
     </xml>
 
     <token name="@symlink_element_identifier@"><![CDATA[
-    ln -f -s '$inputFile' '$inputFile.element_identifier' &&
+    #import re
+    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
+    ln -f -s '$inputFile' '$escaped_element_identifier' &&
     ]]></token>
 
     <token name="@java_options@"><![CDATA[