Mercurial > repos > bornea > saint_preprocessing

comparison SAINT_preprocessing.xml @ 52:8031a47f67c6 draft

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Uploaded
author bornea
date Wed, 08 Jun 2016 10:36:32 -0400
parents 2d78642361c3
children 340cc5988c31
comparison
equal deleted inserted replaced
51:09b89febcf98 52:8031a47f67c6
30 <inputs> 30 <inputs>
31 <param type="select" name="type" label="MaxQuant or Scaffold"> 31 <param type="select" name="type" label="MaxQuant or Scaffold">
32 <option value="MaxQuant">MaxQuant</option> 32 <option value="MaxQuant">MaxQuant</option>
33 <option value="Scaffold">Scaffold</option> 33 <option value="Scaffold">Scaffold</option>
34 </param> 34 </param>
35 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/> 35 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output"/>
36 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/> 36 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
37 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/> 37 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
38 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/> 38 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
39 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/> 39 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
40 <repeat name="bait" title="Bait Create"> 40 <repeat name="bait" title="Bait Create">
48 <data format="txt" name="Inter_file" label="Inter File"/> 48 <data format="txt" name="Inter_file" label="Inter File"/>
49 <data format="txt" name="Prey_file" label="Prey File" /> 49 <data format="txt" name="Prey_file" label="Prey File" />
50 <data format="txt" name="Bait_file" label="Bait File" /> 50 <data format="txt" name="Bait_file" label="Bait File" />
51 </outputs> 51 </outputs>
52 <stdio> 52 <stdio>
53 <regex match="Error: bad bait"
54 source="stdout"
55 level="fatal"
56 description="Error: bad bait"/>
57 <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
58 source="stderr"
59 level="fatal"
60 description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
61 <regex match="bait_temp_file = open(sys.argv[10], 'r')"
62 source="stderr"
63 level="fatal"
64 description="Error: Bait create settings mismatch. Check job settings."/>
53 <regex match="Error|error" 65 <regex match="Error|error"
54 source="stdout" 66 source="stdout"
55 level="fatal" 67 level="fatal"
56 description="Unknown error"/> 68 description="Unknown error"/>
57 <regex match="Error|error" 69 <regex match="Error|error"
58 source="stderr" 70 source="stderr"
59 level="fatal" 71 level="fatal"
60 description="Unknown error"/> 72 description="Unknown error"/>
61 <regex match="Error: bad bait"
62 source="stdout"
63 level="fatal"
64 description="Error: bad bait"/>
65 </stdio> 73 </stdio>
66 74
67 <tests> 75 <tests>
68 <test> 76 <test>
69 <param name="input" value="fa_gc_content_input.fa"/> 77 <param name="input" value="fa_gc_content_input.fa"/>