Mercurial > repos > iuc > rgrnastar

comparison macros.xml @ 28:3e94726bfa9d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
author iuc
date Sun, 11 Feb 2024 00:01:54 +0000
parents 79de45b5069b
children b0f2be869d6d
comparison
equal deleted inserted replaced
27:79de45b5069b 28:3e94726bfa9d
2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@ 2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
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@">2.7.11a</token>
8 <token name="@VERSION_SUFFIX@">4</token> 8 <token name="@VERSION_SUFFIX@">0</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:
14 STAR -h | grep versionGenome 14 STAR -h | grep versionGenome
15 or by looking for the versionGenome parameter in source/parametersDefault 15 or by looking for the versionGenome parameter in source/parametersDefault
16 of STAR's source code --> 16 of STAR's source code -->
17 <token name="@IDX_VERSION@">2.7.4a</token> 17 <token name="@IDX_VERSION@">2.7.4a</token>
18 <token name="@IDX_VERSION_SUFFIX@">1</token> 18 <token name="@IDX_VERSION_SUFFIX@">0</token>
19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> 19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
20 20
21 <xml name="requirements"> 21 <xml name="requirements">
22 <requirements> 22 <requirements>
23 <requirement type="package" version="@TOOL_VERSION@">star</requirement> 23 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
24 <requirement type="package" version="1.16.1">samtools</requirement> 24 <requirement type="package" version="1.18">samtools</requirement>
25 <requirement type="package" version="1.12">gzip</requirement> 25 <requirement type="package" version="1.13">gzip</requirement>
26 <yield /> 26 <yield />
27 </requirements> 27 </requirements>
28 </xml> 28 </xml>
29 29
30 <xml name="edam"> 30 <xml name="edam">
120 #end if 120 #end if
121 #end if 121 #end if
122 #if str($refGenomeSource.genomeSAindexNbases): 122 #if str($refGenomeSource.genomeSAindexNbases):
123 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} 123 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
124 #end if 124 #end if
125 ## Diploid mode
126 #if 'diploidconditional' in $refGenomeSource:
127 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
128 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
129 --genomeTransformType Diploid
130 #end if
131 #end if
125 --runThreadN \${GALAXY_SLOTS:-4} 132 --runThreadN \${GALAXY_SLOTS:-4}
126 ## in bytes 133 ## in bytes
127 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000)) 134 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
128 && 135 &&
129 #end if 136 #end if