Mercurial > repos > bornea > query_crapome

comparison CRAPomeQuery.xml @ 11:659644782ecd draft

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Uploaded
author bornea
date Tue, 19 Apr 2016 11:19:32 -0400
parents becf7fd6d908
children edde2724910f
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10:becf7fd6d908 11:659644782ecd
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <data format="txt" name="CrapomeFile" label="CRAPome File"/> 15 <data format="txt" name="CrapomeFile" label="CRAPome File"/>
16 </outputs> 16 </outputs>
17 <stdio> 17 <stdio>
18 <regex match="TypeError"
19 source="stderr"
20 level="fatal"
21 description="Error: Check input file."/>
18 <regex match="Error|error" 22 <regex match="Error|error"
19 source="stdout" 23 source="stdout"
20 level="fatal" 24 level="fatal"
21 description="Unknown error"/> 25 description="Unknown error"/>
22 <regex match="Error|error" 26 <regex match="Error|error"
23 source="stderr" 27 source="stderr"
24 level="fatal" 28 level="fatal"
25 description="Unknown error"/> 29 description="Unknown error"/>
26 <regex match="Error: bad bait"
27 source="stdout"
28 level="fatal"
29 description="Error: bad bait"/>
30 </stdio> 30 </stdio>
31 <tests> 31 <tests>
32 <test> 32 <test>
33 <param name="input" value="fa_gc_content_input.fa"/> 33 <param name="input" value="fa_gc_content_input.fa"/>
34 <output name="out_file1" file="fa_gc_content_output.txt"/> 34 <output name="out_file1" file="fa_gc_content_output.txt"/>
38 Query CRAPome 38 Query CRAPome
39 ------------- 39 -------------
40 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 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.
41 41
42 **1) Input File** 42 **1) Input File**
43
43 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions. 44 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
44 45
45 **2) Species** 46 **2) Species**
47
46 Please specify species. Supported species are Human and Yeast. 48 Please specify species. Supported species are Human and Yeast.
47 </help> 49 </help>
48 </tool> 50 </tool>