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comparison macros.xml @ 27:79de45b5069b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
author iuc
date Fri, 01 Sep 2023 13:17:29 +0000
parents 3ea5a2a63fa2
children 3e94726bfa9d
comparison
equal deleted inserted replaced
26:3ea5a2a63fa2 27:79de45b5069b
3 whenever you make changes to the @TOOL_VERSION@ token! 3 whenever you make changes to the @TOOL_VERSION@ token!
4 The data manager uses a symlink to this macro file to keep the STAR and 4 The data manager uses a symlink to this macro file to keep the STAR and
5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> 5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
6 <!-- STAR version to be used --> 6 <!-- STAR version to be used -->
7 <token name="@TOOL_VERSION@">2.7.10b</token> 7 <token name="@TOOL_VERSION@">2.7.10b</token>
8 <token name="@VERSION_SUFFIX@">3</token> 8 <token name="@VERSION_SUFFIX@">4</token>
9 <token name="@PROFILE@">21.01</token> 9 <token name="@PROFILE@">21.01</token>
10 <!-- STAR index version compatible with this version of STAR 10 <!-- STAR index version compatible with this version of STAR
11 This is the STAR version that introduced the index structure expected 11 This is the STAR version that introduced the index structure expected
12 by the current version. 12 by the current version.
13 It can be found for any specific version of STAR with: 13 It can be found for any specific version of STAR with:
58 <citation type="doi">10.1093/bioinformatics/bts635</citation> 58 <citation type="doi">10.1093/bioinformatics/bts635</citation>
59 </citations> 59 </citations>
60 </xml> 60 </xml>
61 <xml name="SJDBOPTIONS"> 61 <xml name="SJDBOPTIONS">
62 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> 62 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
63 <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
63 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> 64 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
64 </xml> 65 </xml>
65 <xml name="dbKeyActions"> 66 <xml name="dbKeyActions">
66 <actions> 67 <actions>
67 <expand macro="dbKeyAction"/> 68 <expand macro="dbKeyAction"/>
101 #if 'GTFconditional' in $refGenomeSource: 102 #if 'GTFconditional' in $refGenomeSource:
102 ## GTFconditional exists only in STAR, but not STARsolo 103 ## GTFconditional exists only in STAR, but not STARsolo
103 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 104 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
104 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' 105 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
105 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 106 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
107 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
106 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 108 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
107 --sjdbGTFtagExonParentTranscript Parent 109 --sjdbGTFtagExonParentTranscript Parent
108 #end if 110 #end if
109 #end if 111 #end if
110 #else: 112 #else:
111 ## ref genome selection is less complex for STARsolo cause 113 ## ref genome selection is less complex for STARsolo because
112 ## with-gtf is mandatory there 114 ## with-gtf is mandatory there
113 --sjdbOverhang '${refGenomeSource.sjdbOverhang}' 115 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
114 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}' 116 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
117 --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}'
115 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3': 118 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
116 --sjdbGTFtagExonParentTranscript Parent 119 --sjdbGTFtagExonParentTranscript Parent
117 #end if 120 #end if
118 #end if 121 #end if
119 #if str($refGenomeSource.genomeSAindexNbases): 122 #if str($refGenomeSource.genomeSAindexNbases):
135 '${refGenomeSource.GTFconditional.genomeDir.fields.path}' 138 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
136 ## Handle difference between indices with/without annotations 139 ## Handle difference between indices with/without annotations
137 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf': 140 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
138 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang 141 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
139 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' 142 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
143 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
140 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': 144 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
141 --sjdbGTFtagExonParentTranscript Parent 145 --sjdbGTFtagExonParentTranscript Parent
142 #end if 146 #end if
143 #end if 147 #end if
144 #end if 148 #end if