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comparison create_reference_dataset.xml @ 14:d975e466d443

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Add stdio tag to create_reference_dataset.xml
author Jim Johnson <jj@umn.edu>
date Mon, 10 Jun 2013 05:43:53 -0500
parents 85693cb5339f
children 547d8db4673e
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13:85693cb5339f 14:d975e466d443
7 <requirement type="package" version="2013-05-09">gmap</requirement> 7 <requirement type="package" version="2013-05-09">gmap</requirement>
8 <requirement type="package" version="latest">kent</requirement> 8 <requirement type="package" version="latest">kent</requirement>
9 </requirements> 9 </requirements>
10 <command interpreter="command"> /bin/bash $shscript </command> 10 <command interpreter="command"> /bin/bash $shscript </command>
11 <inputs> 11 <inputs>
12 <param name="ensembl_genome_version" type="text" value="" label="Esembl Genome Version" help="Example: GRCh37"/> 12 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Example: GRCh37"/>
13 <param name="ensembl_version" type="integer" value="" label="Esembl Release Version" help="Example: 71"/> 13 <param name="ensembl_version" type="integer" value="" label="Esembl Release Version" help="Example: 71"/>
14 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Example: hg19"/> 14 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Example: hg19"/>
15 <param name="chromosomes" type="text" value="" label="Chromosomes" help="Example: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/> 15 <param name="chromosomes" type="text" value="" label="Chromosomes" help="Example: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
16 <param name="mt_chromosome" type="text" value="MT" label="Mitochonrial Chromosome" /> 16 <param name="mt_chromosome" type="text" value="MT" label="Mitochonrial Chromosome" />
17 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" /> 17 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" />
19 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" /> 19 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> 22 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
23 </outputs> 23 </outputs>
24 <stdio>
25 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
26 <regex match="Error:"
27 source="both"
28 level="fatal"
29 description="Error running Create DeFuse Reference" />
30
31 </stdio>
24 <configfiles> 32 <configfiles>
25 <configfile name="defuse_config"> 33 <configfile name="defuse_config">
26 #import ast 34 #import ast
27 # 35 #
28 # Configuration file for defuse 36 # Configuration file for defuse