rgrnastar: rg_rnaStar.xml annotate

annotate rg_rnaStar.xml @ 23:a2b0feda6933 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266

author	iuc
date	Fri, 17 Feb 2023 20:03:27 +0000
parents	980d2a2e1180
children	4df95e2d7f61

rev	line source
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1 <tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" 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>
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	3 <macros>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	4 <import>macros.xml</import>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	5 </macros>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	6 <expand macro="edam"/>
16 e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	7 <xrefs>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	8 <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	9 </xrefs>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	10 <expand macro="requirements"/>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	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':
20 91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	55 ## need to check first if its a cached index or from history
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	56 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	57 #if str($refGenomeSource.geneSource) == 'history':
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	58 #if not $refGenomeSource.GTFconditional.sjdbGTFfile:
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	59 ## case of cached index without built-in gene model,
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	60 ## when user does not supply the optional gtf, but
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	61 ## specifies the splice junction overhang
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	62 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	63 #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	64 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	65 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	66 #end if
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	67
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	68 --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	69 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	70 --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	71 #end if
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	72
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	73 ## Output format parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	74
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	75 ## Read tags
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	76 #set read_tags = str($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	77 #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	78 ## 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	79 $read_tags.remove('XS')
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	80 --outSAMstrandField intronMotif
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	81 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	82 #if 'HI' in str($oformat.outSAMattributes):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	83 --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	84 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	85 #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	86 --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	87
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	88 ## Read FLAG
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	89 --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	90
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	91 ## Read MAPQ
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	92 --outSAMmapqUnique ${oformat.outSAMmapqUnique}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	93
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	94 ## Output filter parameters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	95
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	96 ## Basic Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	97 #if str($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	98 #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	99 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	100 #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	101 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	102 #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	103 $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	104 --outSAMunmapped None
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	105 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	106 --outSAMunmapped Within
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	107 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	108 #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	109 ## 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	110 ## with RemoveNoncanonicalUnannotated
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	111 #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	112 $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated')
7 a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	113 #end if
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	114 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	115 #echo ' '.join($filter_options)
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	116
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	117 ## Other Filters
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	118 #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	119 --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	120 --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	121 --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	122 --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	123 --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	124 --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	125 --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	126 --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	127 --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	128 --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	129 --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	130 --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	131 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	132
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	133 ## 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	134 #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	135 ## 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	136 --chimSegmentMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	137 --chimJunctionOverhangMin 12
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	138 --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	139 --alignMatesGapMax 100000
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	140 --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	141 --chimSegmentReadGapMax 3
a70a7eebb435 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c iuc parents: 6 diff changeset	142 --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	143 --peOverlapNbasesMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	144 --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	145 --chimMultimapScoreRange 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	146 --chimMultimapNmax 10
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	147 --chimNonchimScoreDropMin 10
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	148
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	149 #elif str( $algo.params.settingsType ) == 'arriba':
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	150 ## Preset parameters for Arriba
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	151 --peOverlapNbasesMin 10
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	152 --alignSplicedMateMapLminOverLmate 0.5
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	153 --alignSJstitchMismatchNmax 5 -1 5 5
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	154 --chimSegmentMin 10
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	155 --chimJunctionOverhangMin 10
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	156 --chimScoreDropMax 30
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	157 --chimScoreJunctionNonGTAG 0
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	158 --chimScoreSeparation 1
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	159 --chimSegmentReadGapMax 3
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	160 --chimMultimapNmax 50
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	161
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	162 #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	163 ## 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	164
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	165 ## 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	166 --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	167 --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	168 --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	169 --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	170 --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	171 --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	172 --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	173
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	174 ## 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	175 --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	176 --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	177 --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	178 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	179 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	180 --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	181 --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	182 --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	183 --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	184 --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	185 --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	186 --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	187 --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	188 --peOverlapMMp ${algo.params.align.peOverlapMMp}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	189 ## Chimeric alignment parameter options
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	190 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	191 --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	192 --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	193 --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	194 --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	195 --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	196 --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	197 --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	198 --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	199 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	200 #if str($chimOutType) == 'Junctions':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	201 --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	202 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	203 --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	204 #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	205 --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	206 #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	207
99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	208 ## Limits
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	209 @LIMITS@
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	210 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	211 ## 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	212 ## 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	213 ## (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	214 ## 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	215 ## 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	216 ## 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	217 ## --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	218 ## 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	219 #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	220 --chimSegmentMin 12
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	221 #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	222 --chimMultimapNmax 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	223 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	224 #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	225 #end if
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	226
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	227 --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	228 --outBAMsortingBinsN $perf.outBAMsortingBinsN
19 44959aa06aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 27ea73be9aede1e0939ecd7c5f560ac2a630869a" iuc parents: 18 diff changeset	229 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	230 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	231
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	232 ## Handle chimeric options and output
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	233 #if str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	234 --chimOutType $chimOutType
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	235 #if 'Junctions' in str($chimOutType):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	236 --chimOutJunctionFormat 1
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	237 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	238 #end if
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	239
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	240 ##outWig:
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	241 @OUTWIG@
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	242 &&
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	243 ## 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	244 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	245 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	246 ## 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	247 &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	248 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	249 #end if
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	250 ##outWig:
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	251 @OUTWIGOUTPUTS@
1 bc685d13b637 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837 iuc parents: 0 diff changeset	252 ]]></command>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	253
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	254 <inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	255 <!-- 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	256 <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	257 <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	258 <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	259 <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	260 <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	261 </param>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	262 <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	263 <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	264 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	265 <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	266 <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	267 <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	268 </when>
ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	269 <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	270 <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	271 </when>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	272 </conditional>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	273
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	274 <!-- 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	275 <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	276 <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	277 <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	278 <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	279 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	280 <when value="indexed">
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	281 <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	282 <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	283 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	284 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.">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	285 <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model but provide a gtf</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	286 <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</option>
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	287 <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	288 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	289 <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	290 <expand macro="index_selection" with_gene_model="1" />
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	291 <expand macro="quantMode" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	292 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	293 <when value="without-gtf-with-gtf">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	294 <expand macro="index_selection" with_gene_model="0" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	295 <expand macro="SJDBOPTIONS"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	296 <expand macro="quantMode" />
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	297 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	298 <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	299 <expand macro="index_selection" with_gene_model="0" />
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	300 <expand macro="quantModeNoGTF" />
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	301 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	302 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	303 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	304 <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	305 <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	306 <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	307 <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	308 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	309 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	310 <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	311 <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	312 </param>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	313 <when value="with-gtf">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	314 <expand macro="SJDBOPTIONS"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	315 <expand macro="quantMode" />
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	316 </when>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	317 <when value="without-gtf">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	318 <expand macro="quantModeNoGTF" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	319 </when>
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	320 </conditional>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	321 </when>
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 11 diff changeset	322 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	323
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	324 <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	325 <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	326 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	327 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	328 <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	329 <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	330 <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	331 <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	332 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	333 <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	334 <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	335 <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	336 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	337 <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	338 <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	339 <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	340 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	341 <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	342 <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	343 <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	344 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	345 <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	346 <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	347 <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	348 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	349 </when>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	350 </conditional>
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="--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	352 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	353 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	354 <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	355 <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	356 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	357 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	358 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	359 </param>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	360
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	361 <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	362 <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	363 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	364 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	365 with Cufflinks if your sequences come from an unstranded library preparation.">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	366 <expand macro="common_SAM_attributes"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	367 <option value="MC">MC (CIGAR string for mate/next segment)</option>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	368 <option value="XS">XS (strand flag, see parameter help below) </option>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	369 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> <!--This is not the default in STAR-->
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	370 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	371 <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	372 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	373 <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	374 <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	375 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	376 <!-- 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	377 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	378 "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	379 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	380 ‘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	381 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	382
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	383 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	384 <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	385 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	386 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	387 primary?"/> -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	388 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	389 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	390 - according to SAM/BAM specs it means "undefined".
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	391 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	392 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	393 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	394 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
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	395 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 Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	396 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	397 <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	398 <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	399 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	400 <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	401 <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	402 <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	403 <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	404 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	405 <!-- 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	406 <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	407 <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	408 <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	409 <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	410 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 <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	418 <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	419 <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	420 <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	421 <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	422 <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	423 <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	424 <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	425 <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	426 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	427 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	428 <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	429 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	430 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	431
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	432 <!-- Algorithmic settings. -->
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	433 <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	434 <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	435 <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	436 <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	437 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	438 <option value="arriba">Use parameters suggested for Arriba</option>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	439 <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	440 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	441 <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	442 <!-- 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	443 <when value="star_fusion"/>
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	444 <when value="arriba"/>
5 99b17b74a8cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf iuc parents: 3 diff changeset	445
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	446 <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	447 <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	448 <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	449 <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	450 <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	451 <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	452 <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	453 <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	454 <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	455 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	456
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	457 <section name="align" title="Alignment parameters" expanded="false">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	458 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
10 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="--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	460 <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	461 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	462 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	463 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	464 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	465 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	466 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	467 </section>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	468 <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	469 <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	470 <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	471 <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	472 <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	473 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	474 <param argument="--alignEndsType" type="select" label="type of read ends alignment">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	475 <option value="Local">standard local alignment with soft-clipping allowed</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	476 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	477 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	478 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	479 </param>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	480 <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	481 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	482 <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	483 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	484 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	485 <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	486 <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	487 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	488 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	489 <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	490 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	491 <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	492 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	493 <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	494 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	495 <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	496 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	497 <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	498 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	499 <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	500 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	501 <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	502 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	503 <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	504 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	505 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	506 <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	507 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	508 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	509 <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	510 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	511 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	512 </section>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	513 <expand macro="limits" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	514 </when>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	515 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	516 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	517 <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	518 <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." />
19 44959aa06aeb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 27ea73be9aede1e0939ecd7c5f560ac2a630869a" iuc parents: 18 diff changeset	519 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	520 </section>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	521 <expand macro="outWig"/>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	522 </inputs>
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	523
b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	524 <outputs>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	525 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	526 <expand macro="dbKeyActions" />
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	527 </data>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	528
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	529 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	530 <filter>('Junctions' in chimOutType)</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	531 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	532 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	533
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	534 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	535 <expand macro="dbKeyActions" />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	536 </data>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	537
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	538 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	539 <expand macro="dbKeyActions" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	540 </data>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	541
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	542 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" >
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	543 <filter>'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	544 <expand macro="dbKeyActions" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	545 </data>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	546
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	547 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	548 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['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	549 <expand macro="dbKeyActions" />
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	550 <expand macro="outCountActions" />
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	551 </data>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	552 <expand macro="outWigOutputs"/>
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	553 </outputs>
2 ace9f5a2b40f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 iuc parents: 1 diff changeset	554
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	555 <tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	556 <test expect_num_outputs="3">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	557 <conditional name="singlePaired">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	558 <param name="sPaired" value="single" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	559 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	560 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	561 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	562 <param name="geneSource" value="history" />
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	563 <param name="genomeFastaFiles" value="tophat_test.fa.gz" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	564 <param name="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	565 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	566 <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	567 <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	568 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	569 <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	570 <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	571 <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	572 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	573 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	574 <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	575 <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	576 <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	577 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	578 <!-- 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	579 <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	580 <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	581 <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	582 <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	583 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	584 <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	585 <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	586 <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	587 <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	588 <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	589 </conditional>
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 <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	592 <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	593 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	594 <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	595 <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	596 <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	597 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	598 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	599 <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	600 <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	601 <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	602 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	603 <!-- 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	604 <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	605 <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	606 <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	607 <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	608 </conditional>
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="refGenomeSource">
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="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	611 <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	612 <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	613 <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	614 <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	615 <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	616 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	617 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	618 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	619 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	620 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	621 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	622 <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	623 <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	624 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	625 <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	626 <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	627 <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	628 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	629 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	630
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	631 <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	632 <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	633 <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	634 <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	635 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	636 <!-- 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	637 <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	638 <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	639 <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	640 <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	641 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	642 <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	643 <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	644 <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	645 <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	646 <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	647 <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	648 <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	649 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	650 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	651 <param name="quantMode" value="TranscriptomeSAM"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	652 </conditional>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	653 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	654 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	655 <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	656 <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	657 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	658 <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	659 <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	660 <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	661 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	662 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	663
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	664 <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	665 <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	666 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	667 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	668 </test>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	669 <!-- test cached no index but gtf file and GeneCounts TranscriptomeSAM mode -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	670 <test expect_num_outputs="5">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	671 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	672 <param name="sPaired" value="single" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	673 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	674 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	675 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	676 <param name="geneSource" value="indexed" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	677 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	678 <param name="GTFselect" value="without-gtf-with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	679 <param name="genomeDir" value="000" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	680 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	681 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	682 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	683 <param name="quantMode" value="TranscriptomeSAM GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	684 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	685 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	686 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	687 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	688 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	689 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	690 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	691 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	692 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	693 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	694 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	695
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	696 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	697 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	698 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	699 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	700 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	701 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	702 <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	703 <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	704 <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	705 <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	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 <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	708 <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	709 <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	710 <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	711 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	712 <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	713 <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	714 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	715 <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	716 <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	717 <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	718 <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	719 <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	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 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	722 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	723 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	724 <param name="settingsType" value="full" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	725 <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	726 <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	727 <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	728 </section>
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>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 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="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	733 <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	734 <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	735 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	736 <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	737 <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	738 <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	739 <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	740 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	741 <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	742 <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	743 <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	744 <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	745 </conditional>
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="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	747 <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	748 <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	749 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	750 <section name="algo">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	751 <conditional name="params">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	752 <param name="settingsType" value="star_fusion" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	753 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	754 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	755
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	756 <output name="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	757 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	758 <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	759 <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	760 <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	761 <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	762 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	763 <conditional name="refGenomeSource">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	764 <param name="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	765 <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	766 <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	767 </conditional>
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="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	769 <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	770 <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	771 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	772 <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	773 <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	774 <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	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 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	777
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	778 <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	779 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	780 <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	781 <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	782 <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	783 <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	784 </conditional>
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="refGenomeSource">
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="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	787 <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	788 <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	789 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	790 <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	791 <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	792 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	793 <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	794 <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	795 <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	796 <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	797 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	798 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	799 <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	800 <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	801 <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	802 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	803 </section>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	804
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	805 <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	806 <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	807 <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	808 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	809 <!-- 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	810 <!-- 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	811 <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	812 <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	813 <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	814 <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	815 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	816 <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	817 <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	818 <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	819 <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	820 </conditional>
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="twopass">
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="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	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 name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	825 <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	826 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	827 <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	828 <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	829 <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	830 <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	831 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	832 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	833 <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	834 <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	835 <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	836 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	837 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	838
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	839 <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	840 <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	841 <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	842 </test>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	843 <!-- 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	844 <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	845 <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	846 <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	847 <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	848 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	849 <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	850 <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	851 <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	852 <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	853 <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	854 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	855 </conditional>
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="twopass">
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="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	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 name="oformat">
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	860 <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	861 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	862 <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	863 <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	864 <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	865 <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	866 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	867 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	868 <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	869 <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	870 <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	871 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	872 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	873
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	874 <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	875 <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	876 <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	877 </test>
20 91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	878 <!-- test Basic twopass with a built-in gtf index option -->
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	879 <test expect_num_outputs="3">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	880 <conditional name="singlePaired">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	881 <param name="sPaired" value="single" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	882 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	883 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	884 <conditional name="refGenomeSource">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	885 <param name="geneSource" value="indexed" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	886 <conditional name="GTFconditional">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	887 <param name="GTFselect" value="with-gtf" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	888 <param name="genomeDir" value="001" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	889 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	890 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	891 <conditional name="twopass">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	892 <param name="twopassMode" value="Basic" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	893 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	894 <section name="oformat">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	895 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	896 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	897 <section name="filter">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	898 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	899 <conditional name="output_params2">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	900 <param name="output_select2" value="yes" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	901 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	902 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	903 <section name="algo">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	904 <conditional name="params">
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	905 <param name="settingsType" value="full" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	906 </conditional>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	907 </section>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	908
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	909 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	910 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	911 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />
91e0f03268ca "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011" iuc parents: 19 diff changeset	912 </test>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	913 <!-- 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	914 <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	915 <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	916 <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	917 <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	918 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	919 <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	920 <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	921 <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	922 <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	923 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	924 <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	925 <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	926 <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	927 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	928 <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	929 <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	930 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	931 <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	932 <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	933 <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	934 <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	935 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	936 </section>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	937 <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	938 <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	939 <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	940 </conditional>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	941 </section>
9 0a563fd2f22e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7 iuc parents: 8 diff changeset	942
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	943 <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	944 <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	945 <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	946 </test>
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	947 <!-- 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	948 <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	949 <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	950 <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	951 <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	952 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	953 <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	954 <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	955 <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	956 <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	957 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	958 <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	959 <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	960 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	961 <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	962 <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	963 <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	964 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	965 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	966 <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	967 <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	968 <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	969 </test>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	970 <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	971 <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	972 <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	973 <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	974 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	975 <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	976 <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	977 <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	978 <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	979 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	980 <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	981 <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	982 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	983 <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	984 <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	985 <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	986 </conditional>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	987 </section>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	988 <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	989 <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	990 <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	991 </test>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	992 <!-- test paired-end input and outWig -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	993 <test expect_num_outputs="6">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	994 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	995 <param name="sPaired" value="paired" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	996 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	997 <param name="input2" value="tophat_in3.fastqsanger" ftype="fastqsanger" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	998 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	999 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1000 <param name="geneSource" value="history" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1001 <param name="genomeFastaFiles" value="tophat_test.fa" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1002 <param name="genomeSAindexNbases" value="5" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1003 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1004 <param name="GTFselect" value="with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1005 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1006 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1007 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1008 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1009 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1010 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1011 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1012 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1013 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1014 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1015 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1016 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1017 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1018 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1019 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1020 <conditional name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1021 <param name="outWigType" value="wiggle" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1022 <param name="outWigTypeSecondWord" value="read2"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1023 <param name="outWigStrand" value="false" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1024 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1025 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1026 <output name="splice_junctions" file="rnastar_test_splicejunctions_PE.bed"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1027 <output name="mapped_reads" file="rnastar_test_mapped_reads_PE.bam" compare="sim_size" delta="634" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1028 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1029 <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1030 <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1031 </test>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1032 <!-- test paired-end input as collection and outWig stranded -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1033 <test expect_num_outputs="8">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1034 <conditional name="singlePaired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1035 <param name="sPaired" value="paired_collection" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1036 <param name="input" >
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1037 <collection type="paired">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1038 <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1039 <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1040 </collection>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1041 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1042 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1043 <conditional name="refGenomeSource">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1044 <param name="geneSource" value="history" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1045 <param name="genomeFastaFiles" value="tophat_test.fa" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1046 <param name="genomeSAindexNbases" value="5" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1047 <conditional name="GTFconditional">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1048 <param name="GTFselect" value="with-gtf" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1049 <param name="sjdbOverhang" value="75"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1050 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1051 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1052 <param name="quantMode" value="GeneCounts"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1053 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1054 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1055 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1056 <section name="oformat">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1057 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1058 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1059 <section name="algo">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1060 <conditional name="params">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1061 <param name="settingsType" value="default" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1062 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1063 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1064 <conditional name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1065 <param name="outWigType" value="bedGraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1066 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1067
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1068 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1069 <output name="splice_junctions">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1070 <assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1071 <has_n_lines n="2"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1072 <has_line_matching expression="test_chromosome\s+251\s+350\s+1\s+1\s+0\s+24\s+0\s+33"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1073 <has_line_matching expression="test_chromosome\s+401\s+500\s+1\s+1\s+0\s+25\s+0\s+36"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1074 </assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1075 </output>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1076 <output name="mapped_reads" >
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1077 <assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1078 <has_size value="4711" delta="800"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1079 </assert_contents>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1080 </output>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1081 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1082 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1083 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1084 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1085 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1086 </test>
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 16 diff changeset	1087 </tests>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1088 <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	1089 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	1090
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1091 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	1092
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1093 Compatibility Notes
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1094
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1095 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	1096 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	1097
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1098 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	1099
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1100 STAR-Fusion
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	1101
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1102 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	1103 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	1104 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	1105
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1106 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	1107
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1108 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	1109
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1110 - 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	1111
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1112 - 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	1113 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	1114 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	1115 `--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	1116
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1117 - 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	1118 `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	1119
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1120 Arriba
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1121
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1122 Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1123 need to enable chimeric alignment detection by STAR for those datasets to be
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1124 generated. Hence, be sure to select either:
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1125
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1126 Report chimeric alignments?: `As separate tabular "Junctions" output (Junctions)` or Report chimeric alignments?: `Within the BAM output (together with regular alignments; WithinBAM)`.
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1127
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1128 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1129
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1130 - under Output filter criteria,
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 22 diff changeset	1131 Would you like to set additional output filters?: select `Yes` to set
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1132 Maximum number of alignments to output a read's alignment results, plus 1 to 50
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1133
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1134 - under Algorithmic settings, Configure seed, alignment and limits options:
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1135 `use parameters suggested for Arriba`.
980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1136
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1137 Cufflinks
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	1138
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1139 .. class:: infomark
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	1140
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1141 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	1142 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	1143 compatibility issues.
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	1144
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1145 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	1146
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1147 - 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	1148 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	1149 - 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	1150 - 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	1151 - 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	1152 - 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	1153 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	1154
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1155 -----
0 b2326241bb09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef iuc parents: diff changeset	1156
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1157 Attribution
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1158
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1159 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	1160 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	1161 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	1162 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	1163 `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	1164
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1165 .. _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	1166 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1167 .. _Arriba: https://github.com/suhrig/arriba
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1168 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
22 980d2a2e1180 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb iuc parents: 20 diff changeset	1169 .. _parameters: https://arriba.readthedocs.io/en/latest/workflow/
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 9 diff changeset	1170 ]]></help>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: 2 diff changeset	1171 <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	1172 </tool>

Mercurial > repos > iuc > rgrnastar

annotate rg_rnaStar.xml @ 23:a2b0feda6933 draft