Mercurial > repos > iuc > rgrnastar
changeset 7:a70a7eebb435 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c
| author | iuc |
|---|---|
| date | Wed, 16 May 2018 17:31:03 -0400 |
| parents | 2055c2667eb3 |
| children | d5659efd66aa |
| files | macros.xml rg_rnaStar.xml test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test_mapped_reads.bam |
| diffstat | 4 files changed, 34 insertions(+), 19 deletions(-) [+] |
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--- a/macros.xml Thu Mar 01 11:56:28 2018 -0500 +++ b/macros.xml Wed May 16 17:31:03 2018 -0400 @@ -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@">
--- a/rg_rnaStar.xml Thu Mar 01 11:56:28 2018 -0500 +++ b/rg_rnaStar.xml Wed May 16 17:31:03 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="rna_star" name="RNA STAR" version="2.5.2b-2" profile="17.01"> +<tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01"> <description>Gapped-read mapper for RNA-seq data</description> <macros> <import>macros.xml</import> @@ -92,8 +92,11 @@ ## Output parameters #if str( $output_params.output_select ) == "yes": --outSAMattributes $output_params.outSAMattributes - --outSAMstrandField $output_params.outSAMstrandField + #if str( $params.settingsType ) != "star_fusion": + --outSAMstrandField $output_params.outSAMstrandField + #end if --outFilterIntronMotifs $output_params.outFilterIntronMotifs + --outFilterIntronStrands $output_params.outFilterIntronStrands #if str( $output_params.output_params2.output_select2 ) == "yes": --outSAMunmapped $output_params.output_params2.outSAMunmapped --outSAMprimaryFlag $output_params.output_params2.outSAMprimaryFlag @@ -108,6 +111,9 @@ --outFilterScoreMinOverLread "$output_params.output_params2.outFilterScoreMinOverLread" --outFilterMatchNmin "$output_params.output_params2.outFilterMatchNmin" --outFilterMatchNminOverLread "$output_params.output_params2.outFilterMatchNminOverLread" + --outSAMmultNmax "$output_params.output_params2.outSAMmultNmax" + --outSAMtlen "$output_params.output_params2.outSAMtlen" + --outBAMsortingBinsN "$output_params.output_params2.outBAMsortingBinsN" #end if #end if @@ -122,9 +128,9 @@ --alignIntronMax 200000 --twopassMode Basic --twopass1readsN -1 - - ## --chimSegmentReadGapMax 3 ## not an option in STAR 2.4.0 - ## --alignSJstitchMismatchNmax 5 -1 5 5 ## not an option in STAR 2.4.0 + --chimSegmentReadGapMax 3 + --alignSJstitchMismatchNmax 5 -1 5 5 + --outSAMstrandField intronMotif #elif str( $params.settingsType ) == "full": ## Extended parameter options @@ -159,12 +165,16 @@ ## Chimeric alignment parameter options #if str( $params.chim.chim_select ) == "yes": + --chimOutType Junctions SeparateSAMold --chimSegmentMin "$params.chim.chimSegmentMin" --chimScoreMin "$params.chim.chimScoreMin" --chimScoreDropMax "$params.chim.chimScoreDropMax" --chimScoreSeparation "$params.chim.chimScoreSeparation" --chimScoreJunctionNonGTAG "$params.chim.chimScoreJunctionNonGTAG" --chimJunctionOverhangMin "$params.chim.chimJunctionOverhangMin" + --chimMainSegmentMultNmax "$params.chim.chimMainSegmentMultNmax" + --chimMultimapNmax "$params.chim.chimMultimapNmax" + --chimMultimapScoreRange "$params.chim.chimMultimapScoreRange" #end if ## Limits @@ -176,14 +186,9 @@ #end if ## Convert chimeric reads. - #if str($params.settingsType) == "star_fusion" or ( str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0 ): + #if str($params.settingsType) == "full" and str($params.chim.chim_select) == "yes" and int($params.chim.chimSegmentMin) > 0: && - samtools view - -@ \${GALAXY_SLOTS:-4} - -Shb Chimeric.out.sam | - - samtools sort - -@ \${GALAXY_SLOTS:-4} - ChimericSorted + samtools sort -@ \${GALAXY_SLOTS:-4} -o ChimericSorted.bam -O BAM Chimeric.out.sam #end if ]]></command> @@ -269,6 +274,10 @@ <option value="RemoveNoncanonical">Remove alignments with non-canonical junctions</option> <option value="RemoveNoncanonicalUnannotated">Remove alignments with unannotated non-canonical junctions</option> </param> + <param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands"> + <option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option> + <option value="None">No filtering</option> + </param> <!-- Additional output parameter settings. --> <conditional name="output_params2"> @@ -290,6 +299,12 @@ <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/> <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/> <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"/> + <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 –-outFilterMultimapNmax) being output" /> + <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN"> + <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option> + <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> + </param> + <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."/> </when> <when value="no"/> </conditional> @@ -358,6 +373,9 @@ <param argument="--chimScoreSeparation" type="integer" min="0" value="10" label="Minimum difference between the best chimeric score and the next one"/> <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" label="Penalty for a non-GT/AG chimeric junction"/> <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" label="Minimum overhang for a chimeric junction"/> + <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"/> + <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" /> + <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" /> </when> <when value="no"/> </conditional> @@ -389,7 +407,7 @@ </data> <data format="bam" name="chimeric_reads" label="${tool.name} on ${on_string}: chimeric.bam" from_work_dir="ChimericSorted.bam"> - <filter>params['settingsType'] == "star_fusion" or ( params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0 )</filter> + <filter>params['settingsType'] == "full" and params['chim']['chim_select'] == "yes" and params['chim']['chimSegmentMin'] > 0</filter> <actions> <conditional name="refGenomeSource.geneSource"> <when value="indexed"> @@ -581,10 +599,7 @@ **STAR-Fusion** STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running -STAR prior to STAR-Fusion can be pre-selected, with the following exceptions:: - - --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0 - --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0 +STAR prior to STAR-Fusion can be pre-selected. **Attributions**