Mercurial > repos > iuc > data_manager_star_index_builder

comparison data_manager/macros.xml @ 4:6ef6520f14fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 39b9b154845ecf517f7d9e9d76c386b473c3ebd2
author iuc
date Wed, 18 Jul 2018 13:26:12 -0400
parents cdc4d8a998e1
children f5eb9afa8f8a
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3:50ca9af6db2e 4:6ef6520f14fc
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.5.2b">star</requirement> 4 <requirement type="package" version="2.6.0b">star</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="1.8">samtools</requirement>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@FASTQ_GZ_OPTION@"> 8 <token name="@FASTQ_GZ_OPTION@">
9 --readFilesCommand zcat 9 --readFilesCommand zcat
10 </token> 10 </token>
15 </xml> 15 </xml>
16 <xml name="@SJDBOPTIONS@"> 16 <xml name="@SJDBOPTIONS@">
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"/> 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"/>
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"/> 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"/>
19 </xml> 19 </xml>
20 <xml name="dbKeyActions">
21 <actions>
22 <conditional name="refGenomeSource.geneSource">
23 <when value="indexed">
24 <action type="metadata" name="dbkey">
25 <option type="from_data_table" name="rnastar_index2" column="1" offset="0">
26 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
27 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
28 </option>
29 </action>
30 </when>
31 <when value="history">
32 <action type="metadata" name="dbkey">
33 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
34 </action>
35 </when>
36 </conditional>
37 </actions>
38 </xml>
20 </macros> 39 </macros>