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comparison CRAPomeQuery.xml @ 18:edde2724910f draft

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author bornea
date Fri, 29 Apr 2016 15:42:37 -0400
parents 659644782ecd
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17:378fc3676c78 18:edde2724910f
1 <tool id="CRAPomeQuery" name="Query CRAPome"> 1 <tool id="CRAPomeQuery" name="Query CRAPome">
2 <description></description> 2 <description></description>
3 <command interpreter="python">CRAPomeQuery.py $input $species $CrapomeFile \$INSTALL_RUN_PATH/</command> 3 <command interpreter="python">CRAPomeQuery.py $input $species $fasta_db $CrapomeFile \$INSTALL_RUN_PATH/</command>
4 <requirements> 4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> 5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements> 6 </requirements>
7 <inputs> 7 <inputs>
8 <param format="txt" name="input" type="data" label="Prey File or single column list"/> 8 <param format="txt" name="input" type="data" label="Prey File or single column list"/>
9 <param type="select" name="species" label="Species"> 9 <param type="select" name="species" label="Species">
10 <option value="HUMAN">Human</option> 10 <option value="HUMAN">Human</option>
11 <option value="YEAST">Yeast</option> 11 <option value="YEAST">Yeast</option>
12 </param> 12 </param>
13 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
13 </inputs> 14 </inputs>
14 <outputs> 15 <outputs>
15 <data format="txt" name="CrapomeFile" label="CRAPome File"/> 16 <data format="txt" name="CrapomeFile" label="CRAPome File"/>
16 </outputs> 17 </outputs>
17 <stdio> 18 <stdio>
44 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions. 45 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
45 46
46 **2) Species** 47 **2) Species**
47 48
48 Please specify species. Supported species are Human and Yeast. 49 Please specify species. Supported species are Human and Yeast.
50
51 **3) Uniprot Fasta Database**
52
53 A uniprot database can be provided that will be used to get gene names.
49 </help> 54 </help>
50 </tool> 55 </tool>