Mercurial > repos > iuc > rgrnastar
comparison macros.xml @ 27:79de45b5069b draft
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 |
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| 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 |