Mercurial > repos > bornea > saint_preprocessing
comparison SAINT_preprocessing.xml @ 52:8031a47f67c6 draft
Uploaded
author | bornea |
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date | Wed, 08 Jun 2016 10:36:32 -0400 |
parents | 2d78642361c3 |
children | 340cc5988c31 |
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51:09b89febcf98 | 52:8031a47f67c6 |
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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"/> |