Mercurial > repos > bornea > saint_preprocessing_peptideshaker

comparison Protein_report_processing.xml @ 1:e28d0b009178 draft

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author bornea
date Tue, 23 Aug 2016 18:55:39 -0400
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0:5a67d55bb091 1:e28d0b009178
1 <tool id="Protein_report_processig" name="SAINT pre-processing Peptideshaker Report">
2 <description></description>
3 <command interpreter="python">Protein_report_processing.py $input $Bait_file $use_metric $fasta_db $preybool
4 "
5 #for $ba in $bait
6 ${ba.bait1}
7 ${ba.assign}
8 ${ba.T_C}
9 #end for
10 "
11 \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
12 </command>
13 <requirements>
14 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
15 </requirements>
16 <inputs>
17 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" muliple="true"/>
18 <param type="use_metric" name="type" label="Select Report File Value for Qunatification">
19 <option value="#Validated Peptides">#Validated Peptides</option>
20 <option value="#Peptides">#Peptides</option>
21 <option value="#Unique">#Unique</option>
22 <option value="#Validated PSMs">#Validated PSMs</option>
23 <option value="#PSMs">#PSMs</option>
24 </param>
25 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
26 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
27 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
28 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
29 <repeat name="bait" title="Bait Create">
30 <param name="bait1" type="text" size="100" label="Bait"/>
31 <param name="assign" type="text" size="100" label="Group Assignment"/>
32 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
33 </repeat>
34
35 </inputs>
36 <outputs>
37 <data format="txt" name="Inter_file" label="Inter File"/>
38 <data format="txt" name="Prey_file" label="Prey File" />
39 <data format="txt" name="Bait_file" label="Bait File" />
40 </outputs>
41 <stdio>
42 <regex match="Error: bad bait"
43 source="stdout"
44 level="fatal"
45 description="Error: bad bait"/>
46 <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
47 source="stderr"
48 level="fatal"
49 description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
50 <regex match="bait_temp_file = open(sys.argv[10], 'r')"
51 source="stderr"
52 level="fatal"
53 description="Error: Bait create settings mismatch. Check job settings."/>
54 <regex match="Error|error"
55 source="stdout"
56 level="fatal"
57 description="Unknown error"/>
58 <regex match="Error|error"
59 source="stderr"
60 level="fatal"
61 description="Unknown error"/>
62 </stdio>
63
64 <tests>
65 <test>
66 <param name="input" value="fa_gc_content_input.fa"/>
67 <output name="out_file1" file="fa_gc_content_output.txt"/>
68 </test>
69 </tests>
70 <help>
71 </help>
72 </tool>