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comparison nsaf_scoring.xml @ 1:e3625c710dd3 draft

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author bornea
date Wed, 11 May 2016 10:51:03 -0400
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children a2d0d346f07c
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0:46a582eb1ea9 1:e3625c710dd3
1 <tool id="nsaf_scoring" name="NSAF Scoring Table">
2 <description></description>
3 <command interpreter="python">nsaf_scoring.py $list_file $prey_file $crapome $inter_file $outfile \$INSTALL_RUN_PATH/ </command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs>
8 <param format="txt" name="list_file" type="data" label="List File"/>
9 <param format="txt" name="prey_file" type="data" label="Prey File"/>
10 <param format="txt" name="crapome" type="data" label="Crapome File" optional="true"/>
11 <param format="txt" name="inter_file" type="data" label="Inter File" />
12 </inputs>
13 <outputs>
14 <data format="txt" name="outfile" label="NSAF Scored Table"/>
15 </outputs>
16 <stdio>
17 <regex match="ValueError: 'PreyGene' is not in list"
18 source="stdout"
19 level="fatal"
20 description="Error: Check Input file."/>
21 <regex match="Error|error"
22 source="stdout"
23 level="fatal"
24 description="Unknown error"/>
25 <regex match="Error|error"
26 source="stderr"
27 level="fatal"
28 description="Unknown error"/>
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 </help>
38 </tool>