| Previous changeset 13:7e6fd3d0f16e (2016-12-06) Next changeset 15:00fe2ff64467 (2016-12-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f |
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modified:
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 |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_AddCommentsToBam.xml --- a/picard_AddCommentsToBam.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_AddCommentsToBam.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -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}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -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=", $rg_pu, '"') |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_BedToIntervalList.xml --- a/picard_BedToIntervalList.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_BedToIntervalList.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -29,7 +29,7 @@ picard BedToIntervalList - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" SEQUENCE_DICTIONARY="${picard_dict}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CleanSam.xml --- a/picard_CleanSam.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CleanSam.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -9,7 +9,7 @@ @symlink_element_identifier@ picard CleanSam - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" QUIET=true VERBOSITY=ERROR |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectAlignmentSummaryMetrics.xml --- a/picard_CollectAlignmentSummaryMetrics.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectAlignmentSummaryMetrics.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -19,7 +19,7 @@ picard CollectAlignmentSummaryMetrics - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" MAX_INSERT_SIZE=${maxinsert} #for $sequence in $adapters: |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectBaseDistributionByCycle.xml --- a/picard_CollectBaseDistributionByCycle.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectBaseDistributionByCycle.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -21,7 +21,7 @@ picard CollectBaseDistributionByCycle - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" ALIGNED_READS_ONLY="${aligned_reads_only}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectGcBiasMetrics.xml --- a/picard_CollectGcBiasMetrics.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectGcBiasMetrics.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -21,7 +21,7 @@ picard CollectGcBiasMetrics - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" SUMMARY_OUTPUT="${summaryFile}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectInsertSizeMetrics.xml --- a/picard_CollectInsertSizeMetrics.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectInsertSizeMetrics.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -21,7 +21,7 @@ picard CollectInsertSizeMetrics - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" HISTOGRAM_FILE="${histFile}" DEVIATIONS="${deviations}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectRnaSeqMetrics.xml --- a/picard_CollectRnaSeqMetrics.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectRnaSeqMetrics.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -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="${assume_sorted}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_CollectWgsMetrics.xml --- a/picard_CollectWgsMetrics.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_CollectWgsMetrics.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -19,7 +19,7 @@ picard CollectWgsMetrics - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_DownsampleSam.xml --- a/picard_DownsampleSam.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_DownsampleSam.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -9,7 +9,7 @@ @symlink_element_identifier@ picard DownsampleSam - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" PROBABILITY=${probability} RANDOM_SEED=${seed} |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_EstimateLibraryComplexity.xml --- a/picard_EstimateLibraryComplexity.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_EstimateLibraryComplexity.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -10,7 +10,7 @@ picard EstimateLibraryComplexity - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" MIN_IDENTICAL_BASES="${min_identical_bases}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_FilterSamReads.xml --- a/picard_FilterSamReads.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_FilterSamReads.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -11,7 +11,7 @@ picard SortSam - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT=query_sorted_bam.bam SORT_ORDER=queryname VALIDATION_STRINGENCY=LENIENT |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_MarkDuplicates.xml --- a/picard_MarkDuplicates.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_MarkDuplicates.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -10,7 +10,7 @@ picard MarkDuplicates - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" METRICS_FILE="${metrics_file}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_MarkDuplicatesWithMateCigar.xml --- a/picard_MarkDuplicatesWithMateCigar.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_MarkDuplicatesWithMateCigar.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -10,7 +10,7 @@ picard MarkDuplicatesWithMateCigar - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" METRICS_FILE="${metrics_file}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_MeanQualityByCycle.xml --- a/picard_MeanQualityByCycle.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_MeanQualityByCycle.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -20,7 +20,7 @@ picard MeanQualityByCycle - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_NormalizeFasta.xml --- a/picard_NormalizeFasta.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_NormalizeFasta.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -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}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_QualityScoreDistribution.xml --- a/picard_QualityScoreDistribution.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_QualityScoreDistribution.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -20,7 +20,7 @@ picard QualityScoreDistribution - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_ReorderSam.xml --- a/picard_ReorderSam.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_ReorderSam.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -28,7 +28,7 @@ picard ReorderSam - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" REFERENCE="${ref_fasta}" ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_ReplaceSamHeader.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -15,7 +15,7 @@ picard ReplaceSamHeader - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' HEADER="${header}" OUTPUT="${outFile}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_SamToFastq.xml --- a/picard_SamToFastq.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_SamToFastq.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -14,7 +14,7 @@ picard SamToFastq - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' #if str( $output_per_rg ) == "true": OUTPUT_PER_RG=true |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_SortSam.xml --- a/picard_SortSam.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_SortSam.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -15,7 +15,7 @@ @symlink_element_identifier@ picard SortSam - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT='${output}' SORT_ORDER="${sort_order}" QUIET=true |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_ValidateSamFile.xml --- a/picard_ValidateSamFile.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_ValidateSamFile.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -30,7 +30,7 @@ picard ValidateSamFile - INPUT='$inputFile.element_identifier' + INPUT='$escaped_element_identifier' OUTPUT="${outFile}" MODE="${mode}" |
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| diff -r 7e6fd3d0f16e -r 465cbb0cf2eb picard_macros.xml --- a/picard_macros.xml Tue Dec 06 10:04:41 2016 -0500 +++ b/picard_macros.xml Wed Dec 07 14:56:30 2016 -0500 |
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| @@ -17,7 +17,9 @@ </xml> <token name="@symlink_element_identifier@"><![CDATA[ - ln -f -s '$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[ |