rgrnastar: rg_rnaStar.xml annotate

annotate rg_rnaStar.xml @ 18:c772497b2c32 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"

author	iuc
date	Mon, 15 Mar 2021 13:46:07 +0000
parents	e132e7d02a3e
children	44959aa06aeb

rev	line source
16 e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	1 <tool id="rna_star" name="RNA STAR" version="@VERSION@" profile="20.01" license="MIT">
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>
16 e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	3 <xrefs>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	4 <xref type="bio.tools">star</xref>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	5 </xrefs>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	6 <macros>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	7 <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	8 </macros>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	9 <expand macro="requirements"/>
16 e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	10 <expand macro="edam"/>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	11 <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	12
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	13 <!--
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	14 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	15 Hi Gary,
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	16
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	17 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	18 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	19
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	20 Cheers
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	21 Alex
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	22 -->
1 bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 iuc parents: 0 diff changeset	23 <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	24 @TEMPINDEX@
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	25 STAR
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	26 @REFGENOMEHANDLING@
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	27
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	28 --readFilesIn
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	29 #if str($singlePaired.sPaired) == 'paired_collection':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	30 '$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	31
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	32 #if $singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	33 @FASTQ_GZ_OPTION@
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	34 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	35 #else
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	36 '$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	37 #if str($singlePaired.sPaired) == 'paired':
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	38 '$singlePaired.input2'
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
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	41 #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	42 @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	43 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	44 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	45
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	46 --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	47
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	48 ## 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	49 --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	50 #for $sj_input in $twopass.sj_precalculated:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	51 '$sj_input'
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	52 #end for
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	53 #if str($twopass.twopassMode) != 'None':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	54 #if str($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	55 #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	56 ## 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	57 ## 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	58 ## 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	59 --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	60 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	61 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	62 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	63
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	64 --quantMode ${quantmode_output.quantMode}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	65 #if 'TranscriptomeSAM' in str($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	66 --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan}
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	67 #end if
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	68
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	69 ## Output format parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	70
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	71 ## Read tags
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	72 #set read_tags = str($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	73 #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	74 ## 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	75 $read_tags.remove('XS')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	76 --outSAMstrandField intronMotif
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	77 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	78 #if 'HI' in str($oformat.outSAMattributes):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	79 --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	80 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	81 #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	82 --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	83
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	84 ## Read FLAG
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	85 --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	86
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	87 ## Read MAPQ
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	88 --outSAMmapqUnique ${oformat.outSAMmapqUnique}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	89
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	90 ## Output filter parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	91
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	92 ## Basic Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	93 #if str($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	94 #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	95 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	96 #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	97 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	98 #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	99 $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	100 --outSAMunmapped None
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	101 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	102 --outSAMunmapped Within
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	103 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	104 #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	105 ## 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	106 ## with RemoveNoncanonicalUnannotated
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	107 #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	108 $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated')
7 a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	109 #end if
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	110 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	111 #echo ' '.join($filter_options)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	112
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	113 ## Other Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	114 #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	115 --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	116 --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	117 --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	118 --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	119 --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	120 --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	121 --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	122 --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	123 --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	124 --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	125 --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	126 --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	127 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	128
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	129 ## 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	130 #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	131 ## 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	132 --chimSegmentMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	133 --chimJunctionOverhangMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	134 --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	135 --alignMatesGapMax 100000
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	136 --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	137 --chimSegmentReadGapMax 3
a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	138 --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	139 --peOverlapNbasesMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	140 --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	141 --chimMultimapScoreRange 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	142 --chimMultimapNmax 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	143 --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	144
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	145 #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	146 ## 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	147
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	148 ## 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	149 --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	150 --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	151 --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	152 --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	153 --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	154 --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	155 --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	156
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	157 ## 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	158 --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	159 --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	160 --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	161 --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	162 --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	163 --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	164 --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	165 --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	166 --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	167 --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	168 --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	169 --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	170 --peOverlapMMp ${algo.params.align.peOverlapMMp}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	171 ## Chimeric alignment parameter options
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	172 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	173 --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	174 --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	175 --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	176 --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	177 --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	178 --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	179 --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	180 --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	181 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	182 #if str($chimOutType) == 'Junctions':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	183 --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	184 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	185 --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	186 #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	187 --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	188 #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	189
99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	190 ## Limits
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	191 --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	192 --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	193 --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	194 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	195 ## 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	196 ## 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	197 ## (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	198 ## 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	199 ## 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	200 ## 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	201 ## --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	202 ## 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	203 #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	204 --chimSegmentMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	205 #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	206 --chimMultimapNmax 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	207 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	208 #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	209 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	210
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	211 --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	212 --outBAMsortingBinsN $perf.outBAMsortingBinsN
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	213 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	214
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	215 ## Handle chimeric options and output
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	216 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	217 --chimOutType $chimOutType
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	218 #if 'Junctions' in str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	219 --chimOutJunctionFormat 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	220 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	221 #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	222 &&
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	223 ## 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	224 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	225 #if 'TranscriptomeSAM' in str($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	226 ## 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	227 &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	228 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	229 #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	230 ]]></command>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	231
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	232 <inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	233 <!-- 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	234 <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	235 <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	236 <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	237 <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	238 <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	239 </param>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	240 <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	241 <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	242 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	243 <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	244 <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	245 <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	246 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	247 <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	248 <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	249 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	250 </conditional>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	251
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	252 <!-- 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	253 <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	254 <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	255 <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	256 <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	257 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	258 <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	259 <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	260 <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	261 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	262 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	263 <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	264 <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	265 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	266 <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	267 <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	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 <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	270 <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	271 <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	272 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	273 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	274 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	275 <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	276 <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	277 <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	278 <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	279 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	280 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	281 <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	282 <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	283 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	284 <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	285 <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	286 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	287 <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	288 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	289 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	290 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	291
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	292 <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	293 <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	294 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	295 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	296 <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	297 <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	298 <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	299 <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	300 </param>
10 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="None">
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">
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="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	307 <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	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="Basic --twopass1readsN">
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="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	311 <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	312 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	313 <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	314 <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	315 <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	316 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	317 </when>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	318 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	319 <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	320 <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	321 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	322 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	323 <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	324 <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	325 <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	326 <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	327 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	328 <when value="-" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	329 <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	330 <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	331 <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	332 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	333 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	334 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	335 <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	336 <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	337 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	338 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	339 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	340 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	341 <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	342 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	343 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	344 <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	345 <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	346 <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	347 <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	348 </param>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	349
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	350 <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	351 <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	352 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	353 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	354 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	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 <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	363 <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	364 <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	365 <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	366 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	367 <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	368 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	369 <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	370 <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	371 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	372 <!-- 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	373 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	374 "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	375 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	376 ‘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	377 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	378
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	379 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	380 <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	381 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	382 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	383 primary?"/> -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	384 <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	385 <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	386 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	387 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	388 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	389 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	390 <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	391 <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	392 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	393 <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	394 <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	395 <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	396 <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	397 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	398 <!-- 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	399 <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	400 <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	401 <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	402 <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	403 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	404 <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	405 <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	406 <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	407 <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	408 <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	409 <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	410 <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	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 <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	418 <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	419 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	420 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	421 <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	422 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	423 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	424
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	425 <!-- Algorithmic settings. -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	426 <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	427 <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	428 <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	429 <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	430 <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	431 <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	432 </param>
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="default"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	434 <!-- 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	435 <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	436
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	437 <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	438 <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	439 <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	440 <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	441 <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	442 <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	443 <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	444 <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	445 <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	446 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	447
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	448 <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	449 <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	450 <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	451 <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	452 <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	453 <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	454 <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	455 <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	456 <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	457 <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	458 <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	459 <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	460 <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	461 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	462 <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	463 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	464 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	465 <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	466 <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	467 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	468 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	469 <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	470 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	471 <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	472 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	473 <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	474 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	475 <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	476 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	477 <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	478 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	479 <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	480 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	481 <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	482 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	483 <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	484 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	485 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	486 <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	487 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	488 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	489 <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	490 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	491 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	492 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	493 <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	494 <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	495 <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	496 <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	497 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	498 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	499 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	500 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	501 <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	502 <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	503 </section>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	504 </inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	505
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	506 <outputs>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	507 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	508 <expand macro="dbKeyActions" />
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	509 </data>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	510
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	511 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	512 <filter>('Junctions' in chimOutType)</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	513 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	514 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	515
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	516 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	517 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	518 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	519
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	520 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	521 <expand macro="dbKeyActions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	522 </data>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	523
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	524 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" >
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	525 <filter>'TranscriptomeSAM' in quantmode_output['quantMode']</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	526 <expand macro="dbKeyActions" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	527 </data>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	528
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	529 <data name="reads_per_gene" format="tabular" label="${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	530 <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	531 <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	532 </data>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	533 </outputs>
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	534
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	535 <tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	536 <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	537 <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	538 <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	539 <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	540 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	541 <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	542 <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	543 <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	544 <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	545 </conditional>
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="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	547 <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	548 <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	549 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	550 <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	551 <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	552 <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	553 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	554 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	555 <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	556 <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	557 <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	558 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	559 <!-- 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	560 <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	561 <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	562 <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	563 <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	564 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	565 <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	566 <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	567 <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	568 <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	569 <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	570 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	571 </conditional>
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="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	573 <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	574 <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	575 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	576 <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	577 <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	578 <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	579 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	580 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	581 <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	582 <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	583 <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	584 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	585 <!-- 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	586 <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	587 <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	588 <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	589 <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	590 </conditional>
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="refGenomeSource">
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="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	593 <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	594 <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	595 <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	596 <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	597 <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	598 <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	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 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	601 <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	602 <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	603 </conditional>
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="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	605 <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	606 <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	607 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	608 <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	609 <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	610 <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	611 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	612 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	613
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	614 <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	615 <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	616 <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	617 <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	618 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	619 <!-- 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	620 <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	621 <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	622 <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	623 <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	624 </conditional>
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="refGenomeSource">
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="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	627 <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	628 <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	629 <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	630 <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	631 <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	632 <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	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 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	635 <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	636 <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	637 </conditional>
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="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	639 <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	640 <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	641 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	642 <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	643 <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	644 <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	645 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	646 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	647
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	648 <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	649 <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	650 <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	651 <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	652 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	653 <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	654 <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	655 <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	656 <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	657 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	658 <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	659 <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	660 <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	661 <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	662 </conditional>
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="oformat">
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="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	665 <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	666 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	667 <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	668 <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	669 <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	670 <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	671 <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	672 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	673 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	674 <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	675 <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	676 <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	677 <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	678 <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	679 <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	680 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	681 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	682 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	683
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	684 <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	685 <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	686 <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	687 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	688 <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	689 <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	690 <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	691 <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	692 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	693 <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	694 <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	695 <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	696 <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	697 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	698 <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	699 <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	700 <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	701 <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	702 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	703 <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	704 <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	705 <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	706 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	707 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	708
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	709 <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	710 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	711 <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	712 <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	713 <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	714 <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	715 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	716 <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	717 <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	718 <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	719 <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	720 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	721 <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	722 <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	723 <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	724 <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	725 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	726 <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	727 <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	728 <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	729 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	730 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	731
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	732 <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	733 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	734 <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	735 <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	736 <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	737 <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	738 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	739 <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	740 <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	741 <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	742 <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	743 </conditional>
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="oformat">
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="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	746 <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	747 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	748 <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	749 <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	750 <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	751 <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	752 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	753 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	754 <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	755 <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	756 <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	757 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	758 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	759
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	760 <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	761 <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	762 <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	763 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	764 <!-- 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	765 <!-- 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	766 <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	767 <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	768 <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	769 <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	770 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	771 <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	772 <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	773 <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	774 <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	775 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	776 <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	777 <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	778 </conditional>
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="oformat">
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="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	781 <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	782 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	783 <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	784 <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	785 <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	786 <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	787 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	788 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	789 <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	790 <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	791 <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	792 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	793 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	794
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	795 <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	796 <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	797 <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	798 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	799 <!-- 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	800 <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	801 <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	802 <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	803 <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	804 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	805 <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	806 <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	807 <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	808 <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	809 <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	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 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	812 <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	813 <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	814 </conditional>
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="oformat">
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="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	817 <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	818 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	819 <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	820 <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	821 <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	822 <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	823 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	824 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	825 <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	826 <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	827 <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	828 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	829 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	830
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	831 <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	832 <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	833 <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	834 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	835 <!-- 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	836 <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	837 <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	838 <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	839 <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	840 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	841 <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	842 <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	843 <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	844 <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	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 <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	847 <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	848 <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	849 </conditional>
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="oformat">
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="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	852 <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	853 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	854 <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	855 <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	856 <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	857 <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	858 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	859 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	860 <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	861 <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	862 <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	863 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	864 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	865
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	866 <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	867 <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	868 <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	869 </test>
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	870 <!-- test "genomeSAindexNbases" parameter -->
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	871 <test expect_num_outputs="3">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	872 <conditional name="singlePaired">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	873 <param name="sPaired" value="single" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	874 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	875 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	876 <conditional name="refGenomeSource">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	877 <param name="geneSource" value="history" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	878 <param name="genomeFastaFiles" value="tophat_test.fa" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	879 <param name="genomeSAindexNbases" value="14" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	880 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	881 <section name="oformat">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	882 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	883 <param name="outSAMmapqUnique" value="255" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	884 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	885 <section name="algo">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	886 <conditional name="params">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	887 <param name="settingsType" value="default" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	888 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	889 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	890 <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	891 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	892 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	893 </test>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	894 <test expect_num_outputs="3">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	895 <conditional name="singlePaired">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	896 <param name="sPaired" value="single" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	897 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	898 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	899 <conditional name="refGenomeSource">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	900 <param name="geneSource" value="history" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	901 <param name="genomeFastaFiles" value="tophat_test.fa" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	902 <param name="genomeSAindexNbases" value="10" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	903 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	904 <section name="oformat">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	905 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	906 <param name="outSAMmapqUnique" value="255" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	907 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	908 <section name="algo">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	909 <conditional name="params">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	910 <param name="settingsType" value="default" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	911 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	912 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	913 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	914 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	915 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	916 </test>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	917 </tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	918 <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	919 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	920
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	921 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	922
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	923 Compatibility Notes
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	924
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	925 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	926 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	927
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	928 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	929
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	930 STAR-Fusion
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	931
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	932 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	933 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	934 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	935
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	936 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	937
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	938 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	939
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	940 - 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	941
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	942 - 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	943 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	944 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	945 `--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	946
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	947 - 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	948 `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	949
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	950 Cufflinks
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	951
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	952 .. class:: infomark
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	953
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	954 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	955 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	956 compatibility issues.
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	957
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	958 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	959
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	960 - 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	961 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	962 - 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	963 - 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	964 - 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	965 - 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	966 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	967
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	968 -----
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	969
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	970 Attribution
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	971
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	972 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	973 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	974 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	975 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	976 `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	977
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	978 .. _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	979 .. _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	980 .. _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	981 ]]></help>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	982 <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	983 </tool>

Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 18:c772497b2c32 draft