| Previous changeset 4:58b278def57e (2019-09-06) Next changeset 6:178bdbdb6d24 (2019-11-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2082c018009fa73c4afee8313febab13bb807ea8" |
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modified:
rg_rnaStarSolo.xml |
| b |
| diff -r 58b278def57e -r c23da6257d6a rg_rnaStarSolo.xml --- a/rg_rnaStarSolo.xml Fri Sep 06 11:10:22 2019 -0400 +++ b/rg_rnaStarSolo.xml Wed Oct 16 05:24:45 2019 -0400 |
| [ |
| b'@@ -2,7 +2,7 @@\n <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>\n <macros>\n <import>macros.xml</import>\n- <token name="@WRAPPER@"></token>\n+ <token name="@WRAPPER@">1</token>\n </macros>\n <expand macro="requirements"/>\n <expand macro="stdio" >\n@@ -14,13 +14,52 @@\n STAR\n @REFGENOMEHANDLING@\n \n- ## cDNA sequence always goes first, then barcode\n+ ## Check that the input pairs are of the same type\n+ ## otherwise STARsolo will run for a long time and then error out.\n+ ## We consume either repeats of two inputs R1 + R2\n+ ## or a collection of paired reads.\n+\n+ #try\n+ #set $last = None\n+ #for $x in $input_types.input_repeats:\n+ #if str($input_types.use) == "repeat":\n+ #set $r1 = $x.input1\n+ #set $r2 = $x.input2\n+ #elif str($input_types.use) == "list_paired":\n+ #set $r1 = $x.forward\n+ #set $r2 = $x.reverse\n+ #else\n+ Wrong Type\n+ #stop\n+ #end if\n+\n+ #assert $r1.datatype == $r2.datatype\n+\n+ ## Test that all pairs are of the same type\n+ #if $last:\n+ #assert $last.datatype == $r1.datatype\n+ #end if\n+ #set $last = $r1\n+ #end for\n+ #except AssertionError\n+ Input types are not the same!\n+ #stop\n+ #end try\n+\n+ ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]\n+ ## see: Section 3.1 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs\n+ #if str($input_types.use) == "repeat":\n+ #set $reads2 = \',\'.join([ \'%s\' % $x.input2 for $i,$x in enumerate($input_types.input_repeats)])\n+ #set $reads1 = \',\'.join([ \'%s\' % $x.input1 for $i,$x in enumerate($input_types.input_repeats)])\n+ #else if str($input_types.use) == "list_paired"\n+ #set $reads2 = \',\'.join([ \'%s\' % $x.reverse for $i,$x in enumerate($input_types.input_repeats)])\n+ #set $reads1 = \',\'.join([ \'%s\' % $x.forward for $i,$x in enumerate($input_types.input_repeats)])\n+ #end if\n+\n --readFilesIn\n- #set $reads2 = \',\'.join([ \'%s\' % $x.input2 for $i,$x in enumerate($input_repeats)])\n- #set $reads1 = \',\'.join([ \'%s\' % $x.input1 for $i,$x in enumerate($input_repeats)])\n $reads2 $reads1\n \n- #if $input_repeats[0].input1.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ #if $last.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n @FASTQ_GZ_OPTION@\n #end if\n \n@@ -29,8 +68,8 @@\n \n ## 1 - check length of barcode, 0 - do not check\n ## Good for checking custom chemistries\n- --soloBarcodeReadLength 1\n --soloCBwhitelist \'$soloCBwhitelist\'\n+ --soloBarcodeReadLength \'$solo.soloBarcodeReadLength\'\n \n #if str($solo.params.chemistry) == "CR2":\n --soloCBstart 1\n@@ -54,10 +93,21 @@\n --soloUMIdedup \'$solo.soloUMIdedup\'\n ]]></command>\n <inputs>\n- <repeat name="input_repeats" title="Input Pairs" min="1" >\n- <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>\n- <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>\n- </repeat>\n+ <conditional name="input_types" >\n+ <param name="use" type="select" label="Input Type" >\n+ <option value="repeat" >Single files</option>\n+ <option value="list_paired" >List of Pairs</option>\n+ </param>\n+ <when value="repeat">\n+ <repeat name="input_repeats" title="Input Pairs" min="1" >\n+ <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>\n+ <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA fil'..b'epeats" >\n+ <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ </repeat>\n+ <repeat name="input_repeats" >\n+ <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ </repeat>\n+ </conditional>\n+ <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" />\n+ <conditional name="refGenomeSource">\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="SNORD83B.22.fa" />\n+ <param name="genomeSAindexNbases" value="4" />\n+ <conditional name="GTFconditional">\n+ <param name="GTFselect" value="with-gtf" />\n+ <param name="sjdbOverhang" value="75" />\n+ <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/>\n+ </conditional>\n+ </conditional>\n+ <section name="solo" >\n+ <conditional name="params">\n+ <param name="chemistry" value="custom" />\n+ <param name="soloCBstart" value="1" />\n+ <param name="soloCBlen" value="16" />\n+ <param name="soloUMIstart" value="17" />\n+ <param name="soloUMIlen" value="10" />\n+ </conditional>\n+ <param name="soloStrand" value="Forward" />\n+ <param name="soloFeatures" value="GeneFull" />\n+ <param name="soloUMIdedup" value="1MM_Directional" />\n+ </section>\n+ <output name="output_barcodes" >\n+ <assert_contents>\n+ <has_line line="TTTGTCATCTTAGAGC" />\n+ <has_line line="TTTGTCATCTTTCCTC" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="5">\n+ <!-- Same as the test before but with a collection of pairs -->\n+ <conditional name="input_types">\n+ <param name="use" value="list_paired" />\n+ <param name="input_repeats" >\n+ <collection type="list:paired">\n+ <element name="Pair1">\n+ <collection type="paired">\n+ <element name="forward" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ </collection>\n+ </element>\n+ <element name="Pair2">\n+ <collection type="paired">\n+ <element name="forward" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" />\n+ </collection>\n+ </element>\n+ <!-- Planemo does not support more than 2 elements in a list of pairs -->\n+ <!-- <element name="Pair3"> -->\n+ <!-- <element name="forward" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> -->\n+ <!-- <element name="reverse" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> -->\n+ <!-- </element> -->\n+ </collection>\n+ </param>\n+ </conditional>\n <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" />\n <conditional name="refGenomeSource">\n <param name="geneSource" value="history" />\n' |