rgrnastar: rg_rnaStar.xml annotate

annotate rg_rnaStar.xml @ 15:5ec75f5dae3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"

author	iuc
date	Wed, 05 Aug 2020 09:40:33 -0400
parents	41929aa1e7f3
children	e132e7d02a3e

rev	line source
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1 <tool id="rna_star" name="RNA STAR" version="@VERSION@" profile="17.01">
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	2 <description>Gapped-read mapper for RNA-seq data</description>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	3 <macros>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	4 <import>macros.xml</import>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	5 </macros>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	6 <expand macro="requirements"/>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	7 <expand macro="stdio" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	8
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	9 <!--
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	10 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	11 Hi Gary,
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	13 if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	14 If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	15
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	16 Cheers
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	17 Alex
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	18 -->
1 bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 iuc parents: 0 diff changeset	19 <command><![CDATA[
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	20 @TEMPINDEX@
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	21 STAR
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	22 @REFGENOMEHANDLING@
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	23
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	24 --readFilesIn
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	25 #if str($singlePaired.sPaired) == 'paired_collection':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	26 '$singlePaired.input.forward' '$singlePaired.input.reverse'
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	27
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	28 #if $singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	29 @FASTQ_GZ_OPTION@
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	30 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	31 #else
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	32 '$singlePaired.input1'
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	33 #if str($singlePaired.sPaired) == 'paired':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	34 '$singlePaired.input2'
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	35 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	36
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	37 #if $singlePaired.input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	38 @FASTQ_GZ_OPTION@
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	39 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	40 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	41
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	42 --outSAMtype BAM SortedByCoordinate
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	43
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	44 ## Two pass mode
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	45 --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	46 #for $sj_input in $twopass.sj_precalculated:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	47 '$sj_input'
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	48 #end for
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	49 #if str($twopass.twopassMode) != 'None':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	50 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	51 #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	52 ## case of cached index without built-in gene model,
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	53 ## when user does not supply the optional gtf, but
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	54 ## specifies the splice junction overhang
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	55 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	56 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	57 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	58 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	59
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	60 --quantMode ${quantmode_output.quantMode}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	61 #if 'TranscriptomeSAM' in str($quantmode_output.quantMode):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	62 --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan}
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	63 #end if
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	64
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	65 ## Output format parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	66
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	67 ## Read tags
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	68 #set read_tags = str($oformat.outSAMattributes).split(',')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	69 #if 'XS' in str($oformat.outSAMattributes):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	70 ## STAR writes XS tag when --outSAMstrandField intronMotif is used
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	71 $read_tags.remove('XS')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	72 --outSAMstrandField intronMotif
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	73 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	74 #if 'HI' in str($oformat.outSAMattributes):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	75 --outSAMattrIHstart ${oformat.HI_offset}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	76 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	77 #set $tag_names = ' '.join($read_tags)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	78 --outSAMattributes $tag_names
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	79
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	80 ## Read FLAG
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	81 --outSAMprimaryFlag ${oformat.outSAMprimaryFlag}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	82
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	83 ## Read MAPQ
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	84 --outSAMmapqUnique ${oformat.outSAMmapqUnique}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	85
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	86 ## Output filter parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	87
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	88 ## Basic Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	89 #if str($filter.basic_filters) != 'None':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	90 #set $filter_options = str($filter.basic_filters).split(',')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	91 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	92 #set filter_options = []
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	93 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	94 #if 'exclude_unmapped' in $filter_options:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	95 $filter_options.remove('exclude_unmapped')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	96 --outSAMunmapped None
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	97 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	98 --outSAMunmapped Within
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	99 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	100 #if '--outFilterIntronMotifs RemoveNoncanonical' in $filter_options:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	101 ## RemoveNoncanonical excludes a superset of the reads excluded
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	102 ## with RemoveNoncanonicalUnannotated
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	103 #if '--outFilterIntronMotifs RemoveNoncanonicalUnannotated' in $filter_options:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	104 $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated')
7 a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	105 #end if
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	106 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	107 #echo ' '.join($filter_options)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	108
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	109 ## Other Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	110 #if str( $filter.output_params2.output_select2 ) == 'yes':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	111 --outFilterType $filter.output_params2.outFilterType
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	112 --outFilterMultimapScoreRange $filter.output_params2.outFilterMultimapScoreRange
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	113 --outFilterMultimapNmax $filter.output_params2.outFilterMultimapNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	114 --outFilterMismatchNmax $filter.output_params2.outFilterMismatchNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	115 --outFilterMismatchNoverLmax $filter.output_params2.outFilterMismatchNoverLmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	116 --outFilterMismatchNoverReadLmax $filter.output_params2.outFilterMismatchNoverReadLmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	117 --outFilterScoreMin $filter.output_params2.outFilterScoreMin
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	118 --outFilterScoreMinOverLread $filter.output_params2.outFilterScoreMinOverLread
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	119 --outFilterMatchNmin $filter.output_params2.outFilterMatchNmin
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	120 --outFilterMatchNminOverLread $filter.output_params2.outFilterMatchNminOverLread
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	121 --outSAMmultNmax $filter.output_params2.outSAMmultNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	122 --outSAMtlen $filter.output_params2.outSAMtlen
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	123 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	124
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	125 ## Other parameters
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	126 #if str( $algo.params.settingsType ) == 'star_fusion':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	127 ## Preset parameters for STAR-Fusion
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	128 --chimSegmentMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	129 --chimJunctionOverhangMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	130 --alignSJDBoverhangMin 10
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	131 --alignMatesGapMax 100000
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	132 --alignIntronMax 100000
7 a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	133 --chimSegmentReadGapMax 3
a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	134 --alignSJstitchMismatchNmax 5 -1 5 5
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	135 --peOverlapNbasesMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	136 --peOverlapMMp 0.1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	137 --chimMultimapScoreRange 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	138 --chimMultimapNmax 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	139 --chimNonchimScoreDropMin 10
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	140
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	141 #elif str( $algo.params.settingsType ) == 'full':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	142 ## Extended parameter options
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	143
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	144 ## Seed parameter options
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	145 --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	146 --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	147 --seedSearchLmax ${algo.params.seed.seedSearchLmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	148 --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	149 --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	150 --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	151 --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	152
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	153 ## Alignment parameter options
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	154 --alignIntronMin ${algo.params.align.alignIntronMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	155 --alignIntronMax ${algo.params.align.alignIntronMax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	156 --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	157 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	158 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	159 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	160 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	161 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	162 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	163 --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	164 --alignEndsType ${algo.params.align.alignEndsType}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	165 --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	166 --peOverlapMMp ${algo.params.align.peOverlapMMp}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	167 ## Chimeric alignment parameter options
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	168 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	169 --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	170 --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	171 --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	172 --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	173 --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	174 --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	175 --chimFilter $algo.params.chim_settings.chimFilter
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	176 --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	177 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	178 #if str($chimOutType) == 'Junctions':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	179 --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	180 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	181 --chimMultimapNmax 0
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	182 #end if
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	183 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	184 #end if
5 99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	185
99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	186 ## Limits
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	187 --limitOutSJoneRead $algo.params.limits.limitOutSJoneRead
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	188 --limitOutSJcollapsed $algo.params.limits.limitOutSJcollapsed
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	189 --limitSjdbInsertNsj $algo.params.limits.limitSjdbInsertNsj
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	190 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	191 ## Go with STAR's default algorithmic settings,
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	192 ## but we need to provide a reasonable default
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	193 ## (taken from STAR-Fusion)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	194 ## for --chimSegmentMin in case the user enabled chimeric
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	195 ## alignments (the STAR default is 0, which disables chimeric
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	196 ## alignments). For consistency, also set
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	197 ## --chimMultimapNmax to 1 when chimeric alignments are reported
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	198 ## in Junctions format only.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	199 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	200 --chimSegmentMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	201 #if str($chimOutType) == 'Junctions':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	202 --chimMultimapNmax 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	203 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	204 #end if
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	205 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	206
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	207 --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	208 --outBAMsortingBinsN $perf.outBAMsortingBinsN
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	209 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	210
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	211 ## Handle chimeric options and output
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	212 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	213 --chimOutType $chimOutType
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	214 #if 'Junctions' in str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	215 --chimOutJunctionFormat 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	216 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	217 #end if
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	218 &&
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	219 ## recompress BAM output for smaller file size
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	220 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	221 #if 'TranscriptomeSAM' in str($quantmode_output.quantMode):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	222 ## same recompression for optional transcriptome BM
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	223 &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	224 samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	225 #end if
1 bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 iuc parents: 0 diff changeset	226 ]]></command>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	227
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	228 <inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	229 <!-- FASTQ input(s) and options specifically for paired-end data. -->
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	230 <conditional name="singlePaired">
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	231 <param name="sPaired" type="select" label="Single-end or paired-end reads">
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	232 <option value="single" selected="true">Single-end</option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	233 <option value="paired">Paired-end (as individual datasets)</option>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	234 <option value="paired_collection">Paired-end (as collection)</option>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	235 </param>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	236 <when value="single">
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	237 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	238 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	239 <when value="paired">
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	240 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	241 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	242 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	243 <when value="paired_collection">
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	244 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	245 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	246 </conditional>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	247
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	248 <!-- Genome source. -->
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	249 <conditional name="refGenomeSource">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	250 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	251 <option value="indexed" selected="true">Use a built-in index</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	252 <option value="history">Use reference genome from history and create temporary index</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	253 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	254 <when value="indexed">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	255 <conditional name="GTFconditional">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	256 <param name="GTFselect" type="select"
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	257 label="Reference genome with or without an annotation"
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	258 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations.">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	259 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	260 <option value="with-gtf">use genome reference with builtin gene-model</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	261 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	262 <when value="with-gtf">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	263 <expand macro="index_selection" with_gene_model="1" />
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	264 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	265 <when value="without-gtf">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	266 <expand macro="index_selection" with_gene_model="0" />
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	267 <expand macro="@SJDBOPTIONS@" />
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	268 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	269 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	270 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	271 <when value="history">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	272 <expand macro="ref_selection" />
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	273 <conditional name="GTFconditional">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	274 <param name="GTFselect" type="select"
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	275 label="Build index with or without known splice junctions annotation"
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	276 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	277 <option value="without-gtf">build index without gene-model</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	278 <option value="with-gtf">build index with gene-model</option>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	279 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	280 <when value="with-gtf">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	281 <expand macro="@SJDBOPTIONS@" optional="false"/>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	282 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	283 <when value="without-gtf" />
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	284 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	285 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	286 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	287
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	288 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	289 <param argument="--twopassMode" type="select"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	290 label="Use 2-pass mapping for more sensitive novel splice junction discovery"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	291 help="For a study with multiple samples, multisample 2-pass mapping is the most sensitive approach. It involves two separate runs of STAR for each sample, where, in the second run of each sample, the splice junctions found in any sample in the first runs are treated as additional known junctions. If you plan to use the mapping results as input for STAR-Fusion it is recommended that you use at least single-sample 2-pass mapping of all reads.">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	292 <option value="None">No</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	293 <option value="Basic">Yes, perform single-sample 2-pass mapping of all reads</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	294 <option value="Basic --twopass1readsN">Yes, but base novel splice junction detection in the first pass on a subset of all reads (faster, but less sensitive than single-sample 2-pass mode)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	295 <option value="None --sjdbFileChrStartEnd">Yes, I want to use multi-sample 2-pass mapping and I have obtained splice junctions datasets of all samples through previous 1-pass runs of STAR.</option>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	296 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	297 <when value="None">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	298 <param name="twopass_read_subset" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	299 <param name="sj_precalculated" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	300 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	301 <when value="Basic">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	302 <param name="twopass_read_subset" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	303 <param name="sj_precalculated" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	304 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	305 <when value="Basic --twopass1readsN">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	306 <param name="sj_precalculated" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	307 <param argument="--twopass1readsN" name="twopass_read_subset" type="integer" min="1" value="50000" label="Number of reads to map in the first pass"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	308 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	309 <when value="None --sjdbFileChrStartEnd">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	310 <param name="twopass_read_subset" type="hidden" value="" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	311 <param name="sj_precalculated" type="data" multiple="true" format="interval"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	312 label="Pregenerated splice junctions datasets of your samples" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	313 </when>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	314 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	315 <conditional name="quantmode_output">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	316 <param argument="--quantMode" type="select"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	317 label="Per gene/transcript output"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	318 help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	319 <option value="-">No per gene or transcript output</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	320 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	321 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	322 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	323 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	324 <when value="-" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	325 <when value="GeneCounts" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	326 <when value="TranscriptomeSAM">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	327 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	328 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	329 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	330 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	331 <when value="TranscriptomeSAM GeneCounts">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	332 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	333 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	334 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	335 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	336 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	337 <param argument="--chimOutType" type="select"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	338 label="Report chimeric alignments?"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	339 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	340 <option value="">Don't report chimeric alignments</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	341 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	342 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	343 <option value="WithinBAM Junctions">In both forms (WithinBAM Junctions)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	344 </param>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	345
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	346 <section name="oformat" title="BAM output format specification" expanded="true">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	347 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	348 label="Read alignment tags to include in the BAM output"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	349 help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	350 with Cufflinks if your sequences come from an unstranded library preparation.">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	351 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	352 <option value="HI" selected="true">HI (query hit index)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	353 <option value="AS" selected="true">AS (local alignment score)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	354 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	355 <option value="XS">XS (strand flag, see parameter help below) </option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	356 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	357 <option value="MD">MD (string for mismatching positions)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	358 <option value="MC">MC (CIGAR string for mate/next segment)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	359 <option value="jM">jM (intron motifs for all junctions)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	360 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	361 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	362 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	363 <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	364 label="HI tag values should be">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	365 <option value="1" selected="true">one-based</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	366 <option value="0">zero-based</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	367 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	368 <!-- Using - -outSAMprimaryFlag AllBestScore would cause a
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	369 violation of the SAM/BAM spec, which says:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	370 "For each read/contig in a SAM file, it is required that one and
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	371 only one line associated with the read satisfies
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	372 ‘FLAG & 0x900 == 0’.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	373 This line is called the primary line of the read."
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	374
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	375 Thus, this parameter has been removed from the tool interface:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	376 <param argument="- -outSAMprimaryFlag" type="boolean"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	377 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	378 label="Would you like all alignments with the best score labeled
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	379 primary?"/> -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	380 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	381 <param argument="--outSAMmapqUnique" type="integer" value="60" min="30" max="255"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	382 label="MAPQ value for unique mappers"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	383 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	384 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflinks." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	385 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	386 <section name="filter" title="Output filter criteria" expanded="true">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	387 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	388 label="Exclude the following records from the BAM output">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	389 <option value="exclude_unmapped">Unmapped reads</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	390 <option value="--outFilterIntronStrands RemoveInconsistentStrands">Alignments that have junctions with inconsistent strands</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	391 <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Alignments across unannotated non-canonical junctions</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	392 <option value="--outFilterIntronMotifs RemoveNoncanonical">All alignments across non-canonical junctions (recommended for compatibility with Cufflinks)</option>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	393 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	394 <!-- Additional output parameter settings. -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	395 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	396 <param name="output_select2" type="select" label="Would you like to set additional output filters?">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	397 <option value="no" selected="true">No</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	398 <option value="yes">Yes</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	399 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	400 <when value="yes">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	401 <param argument="--outFilterType" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	402 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	403 <param argument="--outFilterMultimapNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	404 <param argument="--outFilterMismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	405 <param argument="--outFilterMismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	406 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	407 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	408 <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"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	409 <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"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	410 <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"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	411 <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" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	412 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	413 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	414 <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>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	415 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	416 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	417 <when value="no"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	418 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	419 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	420
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	421 <!-- Algorithmic settings. -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	422 <section name="algo" title="Algorithmic settings" expanded="true">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	423 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	424 <param name="settingsType" type="select" label="Configure seed, alignment and limits options">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	425 <option value="default" selected="true">Use Defaults</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	426 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	427 <option value="full">Extended parameter list</option>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	428 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	429 <when value="default"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	430 <!-- Set STAR-fusion parameters in command section -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	431 <when value="star_fusion"/>
5 99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	432
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	433 <when value="full">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	434 <section name="seed" title="Seed parameters" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	435 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	436 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	437 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	438 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	439 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	440 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	441 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	442 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	443
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	444 <section name="align" title="Alignment parameters" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	445 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	446 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	447 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	448 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	449 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	450 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	451 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	452 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	453 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	454 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	455 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	456 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	457 label="minimum number of overlap bases to trigger mates merging and realignment" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	458 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	459 label="maximum proportion of mismatched bases in the overlap area" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	460 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	461 <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	462 <param argument="--chimSegmentMin" type="integer" min="1" value="12"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	463 label="Minimum length of chimeric segment"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	464 help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	465 <param argument="--chimScoreMin" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	466 label="Minimum total (summed) score of chimeric segments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	467 <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	468 label="Maximum difference of chimeric score from read length"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	469 <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	470 label="Minimum difference between the best chimeric score and the next one"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	471 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	472 label="Penalty for a non-GT/AG chimeric junction"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	473 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	474 label="Minimum overhang for a chimeric junction"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	475 <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	476 label="Maximum gap in the read sequence between chimeric segments" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	477 <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	478 label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	479 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	480 label="Maximum number of multi-alignments for the main chimeric segment."
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	481 help="A value of 1 prohibits multimapping main segments"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	482 <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	483 label="Maximum number of chimeric multi-alignments"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	484 help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	485 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	486 label="Score range for multi-mapping chimeras"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	487 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" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	488 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	489 <section name="limits" title="Limits" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	490 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	491 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	492 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	493 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	494 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	495 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	496 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	497 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	498 <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. Tweak this if you are facing memory-related errors." />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	499 </section>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	500 </inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	501
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	502 <outputs>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	503 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	504 <expand macro="dbKeyActions" />
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	505 </data>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	506
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	507 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	508 <filter>('Junctions' in chimOutType)</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	509 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	510 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	511
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	512 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	513 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	514 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	515
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	516 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	517 <expand macro="dbKeyActions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	518 </data>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	519
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	520 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" >
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	521 <filter>'TranscriptomeSAM' in quantmode_output['quantMode']</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	522 <expand macro="dbKeyActions" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	523 </data>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	524
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	525 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	526 <filter>'GeneCounts' in quantmode_output['quantMode']</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	527 <expand macro="dbKeyActions" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	528 </data>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	529 </outputs>
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	530
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	531 <tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	532 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	533 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	534 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	535 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	536 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	537 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	538 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	539 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	540 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	541 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	542 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	543 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	544 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	545 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	546 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	547 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	548 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	549 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	550 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	551 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	552 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	553 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	554 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	555 <!-- test with cached genome index -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	556 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	557 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	558 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	559 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	560 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	561 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	562 <param name="geneSource" value="indexed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	563 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	564 <param name="GTFselect" value="with-gtf" />
11 41929aa1e7f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f" iuc parents: 10 diff changeset	565 <param name="genomeDir" value="001" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	566 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	567 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	568 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	569 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	570 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	571 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	572 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	573 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	574 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	575 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	576 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	577 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	578 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	579 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	580 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	581 <!-- test gtf file and GeneCounts mode -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	582 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	583 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	584 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	585 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	586 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	587 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	588 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	589 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	590 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	591 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	592 <param name="GTFselect" value="with-gtf" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	593 <param name="sjdbOverhang" value="75"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	594 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	595 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	596 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	597 <conditional name="quantmode_output">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	598 <param name="quantMode" value="GeneCounts"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	599 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	600 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	601 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	602 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	603 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	604 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	605 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	606 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	607 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	608 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	609
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	610 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	611 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	612 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	613 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
1 bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 iuc parents: 0 diff changeset	614 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	615 <!-- test gtf file and TranscriptomeSAM mode -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	616 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	617 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	618 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	619 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	620 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	621 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	622 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	623 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	624 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	625 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	626 <param name="GTFselect" value="with-gtf" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	627 <param name="sjdbOverhang" value="75"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	628 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	629 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	630 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	631 <conditional name="quantmode_output">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	632 <param name="quantMode" value="TranscriptomeSAM"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	633 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	634 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	635 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	636 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	637 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	638 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	639 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	640 <param name="settingsType" value="default" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	641 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	642 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	643
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	644 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	645 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	646 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	647 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	648 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	649 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	650 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	651 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	652 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	653 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	654 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	655 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	656 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	657 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	658 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	659 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	660 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	661 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	662 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	663 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	664 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	665 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	666 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	667 <param name="outFilterScoreMinOverLread" value="0.9" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	668 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	669 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	670 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	671 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	672 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	673 <section name="seed">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	674 <param name="seed_select" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	675 <param name="seedSearchStartLmax" value="25" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	676 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	677 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	678 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	679
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	680 <output name="output_log" file="rnastar_test2.log" compare="re_match_multiline" />
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	681 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	682 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	683 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	684 <test expect_num_outputs="4">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	685 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	686 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	687 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	688 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	689 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	690 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	691 <param name="genomeFastaFiles" value="test3.ref.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	692 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	693 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	694 <param name="chimOutType" value="Junctions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	695 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	696 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	697 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	698 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	699 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	700 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	701 <param name="settingsType" value="star_fusion" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	702 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	703 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	704
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	705 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	706 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	707 <test expect_num_outputs="4"><!-- tests fastqsanger.gz -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	708 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	709 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	710 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	711 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	712 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	713 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	714 <param name="genomeFastaFiles" value="test3.ref.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	715 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	716 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	717 <param name="chimOutType" value="Junctions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	718 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	719 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	720 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	721 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	722 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	723 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	724 <param name="settingsType" value="star_fusion" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	725 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	726 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	727
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	728 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	729 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	730 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	731 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	732 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	733 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	734 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	735 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	736 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	737 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	738 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	739 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	740 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	741 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	742 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	743 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	744 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	745 <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	746 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	747 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	748 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	749 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	750 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	751 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	752 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	753 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	754 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	755
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	756 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	757 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	758 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	759 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	760 <!-- twopass mode tests -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	761 <!-- test Basic twopass -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	762 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	763 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	764 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	765 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	766 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	767 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	768 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	769 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	770 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	771 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	772 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	773 <param name="twopassMode" value="Basic" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	774 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	775 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	776 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	777 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	778 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	779 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	780 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	781 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	782 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	783 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	784 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	785 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	786 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	787 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	788 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	789 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	790
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	791 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	792 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	793 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	794 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	795 <!-- test Basic twopass without a gtf file option -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	796 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	797 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	798 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	799 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	800 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	801 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	802 <param name="geneSource" value="indexed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	803 <conditional name="GTFconditional">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	804 <param name="GTFselect" value="without-gtf" />
11 41929aa1e7f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f" iuc parents: 10 diff changeset	805 <param name="genomeDir" value="000" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	806 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	807 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	808 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	809 <param name="twopassMode" value="Basic" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	810 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	811 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	812 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	813 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	814 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	815 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	816 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	817 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	818 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	819 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	820 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	821 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	822 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	823 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	824 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	825 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	826
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	827 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	828 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	829 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	830 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	831 <!-- test "multisample" twopass -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	832 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	833 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	834 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	835 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	836 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	837 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	838 <param name="geneSource" value="history" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	839 <param name="genomeFastaFiles" value="tophat_test.fa" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	840 <param name="genomeSAindexNbases" value="5" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	841 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	842 <conditional name="twopass">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	843 <param name="twopassMode" value="None --sjdbFileChrStartEnd" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	844 <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	845 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	846 <section name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	847 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	848 <param name="outSAMmapqUnique" value="255" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	849 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	850 <section name="filter">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	851 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	852 <conditional name="output_params2">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	853 <param name="output_select2" value="yes" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	854 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	855 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	856 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	857 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	858 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	859 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	860 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	861
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	862 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	863 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	864 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	865 </test>
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	866 </tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	867 <help><![CDATA[
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	868 What it does
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	869
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	870 STAR_ is an ultrafast universal RNA-seq aligner.
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	871
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	872 Compatibility Notes
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	873
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	874 STAR has a huge amount of options to filter alignments and to configure the
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	875 exact format of its output.
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	876
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	877 Some tools you may plan to use in your downstream analysis of the results are known to be sensitive to these settings or combinations of them.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	878
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	879 STAR-Fusion
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	880
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	881 STAR-Fusion_ can use the chimeric junctions output of STAR as input, but you
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	882 need to enable chimeric alignment detection by STAR for that dataset to be
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	883 generated. Hence, be sure to select:
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	884
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	885 Report chimeric alignments?: `As separate tabular "Junctions" output (Junctions)`.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	886
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	887 In addition, for best results it is recommended_ that you
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	888
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	889 - use 2-pass mapping for more sensitive novel splice junction discovery
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	890
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	891 - under BAM output format specification,
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	892 Read alignment tags to include in the BAM output: select `XS` as an
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	893 additional tag to generate (this is the equivalent of using
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	894 `--outSAMstrandField intronMotif` on the command line)
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	895
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	896 - under Algorithmic settings, Configure seed, alignment and limits options:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	897 `use parameters suggested for STAR-Fusion`.
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	898
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	899 Cufflinks
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	900
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	901 .. class:: infomark
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	902
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	903 Cufflinks is not considered to be the best tool for use downstream of STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	904 anymore. Consider using Stringtie instead, which also should pose no
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	905 compatibility issues.
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	906
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	907 To avoid compatibility issues with Cufflinks you should:
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	908
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	909 - select XS as a Read alignment tag to include in the BAM output if (and
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	910 only if) your sequenced reads come from an unstranded library prep
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	911 - not select the jM and jI tags for inclusion
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	912 - keep the HI tag selected and
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	913 - select HI tag values should be zero-based
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	914 - exclude All alignments across non-canonical junctions under *Output
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	915 filter criteria -> Exclude the following records from the BAM output*
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	916
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	917 -----
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	918
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	919 Attribution
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	920
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	921 Minor tweaks to output names to suit downstream purposes, toolshed automated
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	922 dependencies and odds and ends of other code and documentation comprising
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	923 this tool were originally written by Ross Lazarus and have been licensed under
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	924 the creative commons
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	925 `BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	926
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	927 .. _STAR: https://github.com/alexdobin/STAR
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	928 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	929 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	930 ]]></help>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	931 <expand macro="citations"/>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	932 </tool>

Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 15:5ec75f5dae3c draft