Mercurial > repos > iuc > data_manager_star_index_builder

comparison data_manager/macros.xml @ 6:54cddd903437 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/data_managers/data_manager_star_index_builder commit b3b5e4587d85ab790b78a35d851f57f34627dc0b
author iuc
date Thu, 11 Jul 2019 11:35:38 -0400
parents 1bd6dc820044
children 9a231bb19a3b
comparison
equal deleted inserted replaced
5:1bd6dc820044 6:54cddd903437
1 <macros> 1 <macros>
2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
3 whenever you make changes to the following two version tokens!
4 The data manager uses a symlink to this macro file to keep the versions in
5 sync. -->
6 <!-- STAR version to be used -->
7 <token name="@VERSION@">2.7.1a</token>
8 <!-- STAR index version compatible with this version of STAR
9 This is the STAR version that introduced the index structure expected
10 by the current version.
11 It can be found for any specific version of STAR with:
12 STAR -h | grep versionGenome
13 or by looking for the versionGenome parameter in source/parametersDefault
14 of STAR's source code -->
15 <token name="@IDX_VERSION@">2.7.1a</token>
16
2 <xml name="requirements"> 17 <xml name="requirements">
3 <requirements> 18 <requirements>
4 <requirement type="package" version="2.6.0b">star</requirement> 19 <requirement type="package" version="@VERSION@">star</requirement>
5 <requirement type="package" version="1.8">samtools</requirement> 20 <requirement type="package" version="1.9">samtools</requirement>
6 </requirements> 21 </requirements>
7 </xml> 22 </xml>
23
24 <xml name="index_selection" token_with_gene_model="1">
25 <param argument="--genomeDir" name="genomeDir" type="select"
26 label="Select reference genome"
27 help="If your genome of interest is not listed, contact the Galaxy team">
28 <options from_data_table="rnastar_index2_versioned">
29 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
30 <filter type="static_value" column="5" value="@IDX_VERSION@" />
31 <filter type="sort_by" column="2" />
32 <validator type="no_options" message="No indexes are available for the selected input dataset" />
33 </options>
34 </param>
35 </xml>
36
8 <token name="@FASTQ_GZ_OPTION@"> 37 <token name="@FASTQ_GZ_OPTION@">
9 --readFilesCommand zcat 38 --readFilesCommand zcat
10 </token> 39 </token>
11 <xml name="citations"> 40 <xml name="citations">
12 <citations> 41 <citations>
13 <citation type="doi">10.1093/bioinformatics/bts635</citation> 42 <citation type="doi">10.1093/bioinformatics/bts635</citation>
14 </citations> 43 </citations>
15 </xml> 44 </xml>
16 <xml name="@SJDBOPTIONS@"> 45 <xml name="@SJDBOPTIONS@" token_optional="true">
17 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="true" help="Exon junction information for mapping splices"/> 46 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
18 <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"/> 47 <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"/>
19 </xml> 48 </xml>
20 <xml name="dbKeyActions"> 49 <xml name="dbKeyActions">
21 <actions> 50 <actions>
22 <conditional name="refGenomeSource.geneSource"> 51 <conditional name="refGenomeSource.geneSource">
23 <when value="indexed"> 52 <when value="indexed">
24 <action type="metadata" name="dbkey"> 53 <action type="metadata" name="dbkey">
25 <option type="from_data_table" name="rnastar_index2" column="1" offset="0"> 54 <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
26 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 55 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
27 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> 56 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
28 </option> 57 </option>
29 </action> 58 </action>
30 </when> 59 </when>