| Previous changeset 6:2055c2667eb3 (2018-03-01) Next changeset 8:d5659efd66aa (2018-06-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c |
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modified:
macros.xml rg_rnaStar.xml test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test_mapped_reads.bam |
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| diff -r 2055c2667eb3 -r a70a7eebb435 macros.xml --- a/macros.xml Thu Mar 01 11:56:28 2018 -0500 +++ b/macros.xml Wed May 16 17:31:03 2018 -0400 |
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| @@ -1,8 +1,8 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.5.2b">star</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="2.6.0b">star</requirement> + <requirement type="package" version="1.8">samtools</requirement> </requirements> </xml> <token name="@FASTQ_GZ_OPTION@"> |
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| diff -r 2055c2667eb3 -r a70a7eebb435 rg_rnaStar.xml --- a/rg_rnaStar.xml Thu Mar 01 11:56:28 2018 -0500 +++ b/rg_rnaStar.xml Wed May 16 17:31:03 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01">\n+<tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01">\n <description>Gapped-read mapper for RNA-seq data</description>\n <macros>\n <import>macros.xml</import>\n@@ -92,8 +92,11 @@\n ## Output parameters\n #if str( $output_params.output_select ) == "yes":\n --outSAMattributes $output_params.outSAMattributes\n- --outSAMstrandField $output_params.outSAMstrandField\n+ #if str( $params.settingsType ) != "star_fusion":\n+ --outSAMstrandField $output_params.outSAMstrandField\n+ #end if\n --outFilterIntronMotifs $output_params.outFilterIntronMotifs\n+ --outFilterIntronStrands $output_params.outFilterIntronStrands\n #if str( $output_params.output_params2.output_select2 ) == "yes":\n --outSAMunmapped $output_params.output_params2.outSAMunmapped\n --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag\n@@ -108,6 +111,9 @@\n --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread"\n --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin"\n --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread"\n+ --outSAMmultNmax "$output_params.output_params2.outSAMmultNmax"\n+ --outSAMtlen "$output_params.output_params2.outSAMtlen"\n+ --outBAMsortingBinsN "$output_params.output_params2.outBAMsortingBinsN"\n #end if\n #end if\n \n@@ -122,9 +128,9 @@\n --alignIntronMax 200000\n --twopassMode Basic\n --twopass1readsN -1\n-\n- ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0\n- ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0\n+ --chimSegmentReadGapMax 3\n+ --alignSJstitchMismatchNmax 5 -1 5 5\n+ --outSAMstrandField intronMotif\n \n #elif str( $params.settingsType ) == "full":\n ## Extended parameter options\n@@ -159,12 +165,16 @@\n \n ## Chimeric alignment parameter options\n #if str( $params.chim.chim_select ) == "yes":\n+ --chimOutType Junctions SeparateSAMold\n --chimSegmentMin "$params.chim.chimSegmentMin"\n --chimScoreMin "$params.chim.chimScoreMin"\n --chimScoreDropMax "$params.chim.chimScoreDropMax"\n --chimScoreSeparation "$params.chim.chimScoreSeparation"\n --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG"\n --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin"\n+ --chimMainSegmentMultNmax "$params.chim.chimMainSegmentMultNmax"\n+ --chimMultimapNmax "$params.chim.chimMultimapNmax"\n+ --chimMultimapScoreRange "$params.chim.chimMultimapScoreRange"\n #end if\n \n ## Limits\n@@ -176,14 +186,9 @@\n #end if\n \n ## Convert chimeric reads.\n- #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ):\n+ #if str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0:\n &&\n- samtools view\n- -@ \\${GALAXY_SLOTS:-4}\n- -Shb Chimeric.out.sam |\n- \n- samtools sort\n- -@ \\${GALAXY_SLOTS:-4} - ChimericSorted\n+ samtools sort -@ \\${GALAXY_SLOTS:-4} -o ChimericSorted.bam -O BAM Chimeric.out.sam\n #end if\n ]]></command>\n \n@@ -269,6 +274,10 @@\n <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option>\n <option value="RemoveNoncanonicalUnannotate'..b'atched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>\n <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>\n+ <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to \xe2\x80\x93-outFilterMultimapNmax) being output" />\n+ <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">\n+ <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>\n+ <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>\n+ </param>\n+ <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50."/>\n </when>\n <when value="no"/>\n </conditional>\n@@ -358,6 +373,9 @@\n <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/>\n <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/>\n <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/>\n+ <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10" label="Maximum number of multi-alignments for the main chimeric segment." help="A value of 1 prohibits multimapping main segments"/>\n+ <param argument="--chimMultimapNmax" type="integer" min="0" value="0" label="Maximum number of chimeric multi-alignments" help="A value of 0 (the default) only considers unique alignments" />\n+ <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" label="Score range for multi-mapping chimeras" help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />\n </when>\n <when value="no"/>\n </conditional>\n@@ -389,7 +407,7 @@\n </data>\n \n <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam">\n- <filter>params[\'settingsType\'] == "star_fusion" or ( params[\'settingsType\'] == "full" and params[\'chim\'][\'chim_select\'] == "yes" and params[\'chim\'][\'chimSegmentMin\'] > 0 )</filter>\n+ <filter>params[\'settingsType\'] == "full" and params[\'chim\'][\'chim_select\'] == "yes" and params[\'chim\'][\'chimSegmentMin\'] > 0</filter>\n <actions>\n <conditional name="refGenomeSource.geneSource">\n <when value="indexed">\n@@ -581,10 +599,7 @@\n **STAR-Fusion**\n \n STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running\n-STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::\n-\n- --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0\n- --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0\n+STAR prior to STAR-Fusion can be pre-selected.\n \n **Attributions**\n \n' |
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| diff -r 2055c2667eb3 -r a70a7eebb435 test-data/rnastar_test2_mapped_reads.bam |
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| Binary file test-data/rnastar_test2_mapped_reads.bam has changed |
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| diff -r 2055c2667eb3 -r a70a7eebb435 test-data/rnastar_test_mapped_reads.bam |
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| Binary file test-data/rnastar_test_mapped_reads.bam has changed |