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comparison MergeFiles.xml @ 2:fc8b0358acac draft

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author bornea
date Wed, 27 Jul 2016 16:21:39 -0400
parents ac70e256399c
children c1b96e4abf8d
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1:ac70e256399c 2:fc8b0358acac
1 <tool id="MergeScaffold" name="Merge Scaffold"> 1 <tool id="MergeScaffold" name="Merge Scaffold">
2 <description></description> 2 <description></description>
3 <command interpreter="python">MergeFiles.py $input1 $input2 $input3 $baitfile $merged \$INSTALL_RUN_PATH/</command> 3 <command interpreter="python">MergeFiles.py $input1 $input2 $input3 $baitfile $merged</command>
4 <requirements>
5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
6 </requirements>
7 <inputs> 4 <inputs>
8 <param format="txt" name="input1" type="data" label="Scaffold Output 1"/> 5 <param format="txt" name="input1" type="data" label="Scaffold Output 1"/>
9 <param format="txt" name="input2" type="data" label="Scaffold Output 2"/> 6 <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"/> 7 <param format="txt" name="input3" type="data" label="Scaffold Output 3" optional = "true"/>
11 <param format="txt" name="baitfile" type="data" label="baitfile"/> 8 <param format="txt" name="baitfile" type="data" label="baitfile"/>
32 <param name="input" value="fa_gc_content_input.fa"/> 29 <param name="input" value="fa_gc_content_input.fa"/>
33 <output name="out_file1" file="fa_gc_content_output.txt"/> 30 <output name="out_file1" file="fa_gc_content_output.txt"/>
34 </test> 31 </test>
35 </tests> 32 </tests>
36 <help> 33 <help>
37 Query CRAPome 34 This program will merge either 2 or 3 scaffold sample report files together.
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> 35 </help>
47 </tool> 36 </tool>