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comparison MergeFiles.xml @ 1:ac70e256399c draft

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author bornea
date Tue, 26 Jul 2016 16:17:25 -0400
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0:84564ae1cca1 1:ac70e256399c
1 <tool id="MergeScaffold" name="Merge Scaffold">
2 <description></description>
3 <command interpreter="python">MergeFiles.py $input1 $input2 $input3 $baitfile $merged \$INSTALL_RUN_PATH/</command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs>
8 <param format="txt" name="input1" type="data" label="Scaffold Output 1"/>
9 <param format="txt" name="input2" type="data" label="Scaffold Output 2"/>
10 <param format="txt" name="input3" type="data" label="Scaffold Output 3" optional = "true"/>
11 <param format="txt" name="baitfile" type="data" label="baitfile"/>
12 </inputs>
13 <outputs>
14 <data format="txt" name="merged" label="Merged Scaffold Report"/>
15 </outputs>
16 <stdio>
17 <regex match="Error|error"
18 source="stdout"
19 level="fatal"
20 description="Unknown error"/>
21 <regex match="Error|error"
22 source="stderr"
23 level="fatal"
24 description="Unknown error"/>
25 <regex match="Error: bad bait"
26 source="stdout"
27 level="fatal"
28 description="Error: bad bait"/>
29 </stdio>
30 <tests>
31 <test>
32 <param name="input" value="fa_gc_content_input.fa"/>
33 <output name="out_file1" file="fa_gc_content_output.txt"/>
34 </test>
35 </tests>
36 <help>
37 Query CRAPome
38 -------------
39 This program will read in a SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions (e.g. "P00533" or "EGFR_HUMAN"), query the CRAPome database (v1.1) http://crapome.org, and return a file specifying the prevalence of each protein in the CRAPome.
40
41 **1) Input File**
42 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
43
44 **2) Species**
45 Please specify species. Supported species are Human and Yeast.
46 </help>
47 </tool>