Mercurial > repos > iuc > rna_starsolo
changeset 2:3a1253ee137b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
| author | iuc |
|---|---|
| date | Tue, 27 Aug 2019 05:58:14 -0400 |
| parents | e613048778d9 |
| children | 61cb2042581a |
| files | macros.xml rg_rnaStarSolo.xml test-data/41737_R1.fastq.sub240k.gz test-data/41737_R1_sub240k.fastq.gz test-data/41737_R2.fastq.sub240k.gz test-data/41737_R2_sub240k.fastq.gz |
| diffstat | 6 files changed, 70 insertions(+), 16 deletions(-) [+] |
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--- a/macros.xml Sat Aug 17 09:37:54 2019 -0400 +++ b/macros.xml Tue Aug 27 05:58:14 2019 -0400 @@ -88,7 +88,7 @@ && #end if ]]></token> - <token name="@REFGENOMEHANDLING" ><![CDATA[ + <token name="@REFGENOMEHANDLING@" ><![CDATA[ --runThreadN \${GALAXY_SLOTS:-4} --genomeLoad NoSharedMemory --genomeDir @@ -97,7 +97,7 @@ #else: '${refGenomeSource.GTFconditional.genomeDir.fields.path}' ## Handle difference between indices with/without annotations - #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': + #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf': #if $refGenomeSource.GTFconditional.sjdbGTFfile: --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' @@ -114,6 +114,7 @@ <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> + <yield /> </stdio> </xml> <xml name="refgenomehandling" > @@ -132,10 +133,10 @@ </param> <when value="with-gtf"> <expand macro="index_selection" with_gene_model="1" /> - <expand macro="@SJDBOPTIONS@" /> </when> <when value="without-gtf"> <expand macro="index_selection" with_gene_model="0" /> + <expand macro="@SJDBOPTIONS@" /> </when> </conditional> </when>
--- a/rg_rnaStarSolo.xml Sat Aug 17 09:37:54 2019 -0400 +++ b/rg_rnaStarSolo.xml Tue Aug 27 05:58:14 2019 -0400 @@ -2,10 +2,12 @@ <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description> <macros> <import>macros.xml</import> - <token name="@WRAPPER@"></token> + <token name="@WRAPPER@">1</token> </macros> <expand macro="requirements"/> - <expand macro="stdio" /> + <expand macro="stdio" > + <regex match="Segmentation fault" source="both" level="fatal" /> + </expand> <command><![CDATA[ @TEMPINDEX@ @@ -14,8 +16,11 @@ ## cDNA sequence always goes first, then barcode --readFilesIn - '$input2' '$input1' - #if $input1.is_of_type('fastq.gz', 'fastqsanger.gz'): + #set $reads2 = ','.join([ '%s' % $x.input2 for $i,$x in enumerate($input_repeats)]) + #set $reads1 = ','.join([ '%s' % $x.input1 for $i,$x in enumerate($input_repeats)]) + $reads2 $reads1 + + #if $input_repeats[0].input1.is_of_type('fastq.gz', 'fastqsanger.gz'): @FASTQ_GZ_OPTION@ #end if @@ -49,10 +54,11 @@ --soloUMIdedup '$solo.soloUMIdedup' ]]></command> <inputs> - <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> - <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/> + <repeat name="input_repeats" title="Input Pairs" min="1" > + <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/> + <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> + </repeat> <param format="txt,tsv" argument="--soloCBwhitelist" type="data" label="RNA-Seq Cell Barcode Whitelist" /> - <expand macro="refgenomehandling" /> <section name="solo" title="Advanced Settings" expanded="true"> <conditional name="params"> @@ -106,13 +112,15 @@ </outputs> <tests> <test expect_num_outputs="5"> - <param name="input1" value="41737_R1.fastq.sub240k.gz" ftype="fastqsanger.gz" /> - <param name="input2" value="41737_R2.fastq.sub240k.gz" ftype="fastqsanger.gz" /> + <repeat name="input_repeats" > + <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + </repeat> <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> - <param name="genomeSAindexNbases" value="5" /> + <param name="genomeSAindexNbases" value="4" /> <conditional name="GTFconditional"> <param name="GTFselect" value="with-gtf" /> <param name="sjdbOverhang" value="75"/> @@ -145,13 +153,58 @@ </output> </test> <test expect_num_outputs="5"> - <param name="input1" value="41737_R1.fastq.sub240k.gz" ftype="fastqsanger.gz" /> - <param name="input2" value="41737_R2.fastq.sub240k.gz" ftype="fastqsanger.gz" /> + <repeat name="input_repeats" > + <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + </repeat> <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> <conditional name="refGenomeSource"> <param name="geneSource" value="history" /> <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> - <param name="genomeSAindexNbases" value="5" /> + <param name="genomeSAindexNbases" value="4" /> + <conditional name="GTFconditional"> + <param name="GTFselect" value="with-gtf" /> + <param name="sjdbOverhang" value="75" /> + <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/> + </conditional> + </conditional> + <section name="solo" > + <conditional name="params"> + <param name="chemistry" value="custom" /> + <param name="soloCBstart" value="1" /> + <param name="soloCBlen" value="16" /> + <param name="soloUMIstart" value="17" /> + <param name="soloUMIlen" value="10" /> + </conditional> + <param name="soloStrand" value="Forward" /> + <param name="soloFeatures" value="GeneFull" /> + <param name="soloUMIdedup" value="1MM_Directional" /> + </section> + <output name="output_barcodes" > + <assert_contents> + <has_line line="TTTGTCATCTTAGAGC" /> + <has_line line="TTTGTCATCTTTCCTC" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="5"> + <repeat name="input_repeats" > + <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + </repeat> + <repeat name="input_repeats" > + <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + </repeat> + <repeat name="input_repeats" > + <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> + </repeat> + <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> + <conditional name="refGenomeSource"> + <param name="geneSource" value="history" /> + <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> + <param name="genomeSAindexNbases" value="4" /> <conditional name="GTFconditional"> <param name="GTFselect" value="with-gtf" /> <param name="sjdbOverhang" value="75" />