annotate Protein_report_processing.xml @ 2:058b06fd2c17 draft

Uploaded
author bornea
date Tue, 23 Aug 2016 18:55:58 -0400
parents e28d0b009178
children ae7aad717696
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
e28d0b009178 Uploaded
bornea
parents:
diff changeset
1 <tool id="Protein_report_processig" name="SAINT pre-processing Peptideshaker Report">
e28d0b009178 Uploaded
bornea
parents:
diff changeset
2 <description></description>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
3 <command interpreter="python">Protein_report_processing.py $input $Bait_file $use_metric $fasta_db $preybool
e28d0b009178 Uploaded
bornea
parents:
diff changeset
4 "
e28d0b009178 Uploaded
bornea
parents:
diff changeset
5 #for $ba in $bait
e28d0b009178 Uploaded
bornea
parents:
diff changeset
6 ${ba.bait1}
e28d0b009178 Uploaded
bornea
parents:
diff changeset
7 ${ba.assign}
e28d0b009178 Uploaded
bornea
parents:
diff changeset
8 ${ba.T_C}
e28d0b009178 Uploaded
bornea
parents:
diff changeset
9 #end for
e28d0b009178 Uploaded
bornea
parents:
diff changeset
10 "
e28d0b009178 Uploaded
bornea
parents:
diff changeset
11 \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
e28d0b009178 Uploaded
bornea
parents:
diff changeset
12 </command>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
13 <requirements>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
14 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
15 </requirements>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
16 <inputs>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
17 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" muliple="true"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
18 <param type="use_metric" name="type" label="Select Report File Value for Qunatification">
e28d0b009178 Uploaded
bornea
parents:
diff changeset
19 <option value="#Validated Peptides">#Validated Peptides</option>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
20 <option value="#Peptides">#Peptides</option>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
21 <option value="#Unique">#Unique</option>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
22 <option value="#Validated PSMs">#Validated PSMs</option>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
23 <option value="#PSMs">#PSMs</option>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
24 </param>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
25 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
26 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
27 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
28 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
29 <repeat name="bait" title="Bait Create">
e28d0b009178 Uploaded
bornea
parents:
diff changeset
30 <param name="bait1" type="text" size="100" label="Bait"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
31 <param name="assign" type="text" size="100" label="Group Assignment"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
32 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
33 </repeat>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
34
e28d0b009178 Uploaded
bornea
parents:
diff changeset
35 </inputs>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
36 <outputs>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
37 <data format="txt" name="Inter_file" label="Inter File"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
38 <data format="txt" name="Prey_file" label="Prey File" />
e28d0b009178 Uploaded
bornea
parents:
diff changeset
39 <data format="txt" name="Bait_file" label="Bait File" />
e28d0b009178 Uploaded
bornea
parents:
diff changeset
40 </outputs>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
41 <stdio>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
42 <regex match="Error: bad bait"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
43 source="stdout"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
44 level="fatal"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
45 description="Error: bad bait"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
46 <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
47 source="stderr"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
48 level="fatal"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
49 description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
50 <regex match="bait_temp_file = open(sys.argv[10], 'r')"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
51 source="stderr"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
52 level="fatal"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
53 description="Error: Bait create settings mismatch. Check job settings."/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
54 <regex match="Error|error"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
55 source="stdout"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
56 level="fatal"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
57 description="Unknown error"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
58 <regex match="Error|error"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
59 source="stderr"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
60 level="fatal"
e28d0b009178 Uploaded
bornea
parents:
diff changeset
61 description="Unknown error"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
62 </stdio>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
63
e28d0b009178 Uploaded
bornea
parents:
diff changeset
64 <tests>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
65 <test>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
66 <param name="input" value="fa_gc_content_input.fa"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
67 <output name="out_file1" file="fa_gc_content_output.txt"/>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
68 </test>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
69 </tests>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
70 <help>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
71 </help>
e28d0b009178 Uploaded
bornea
parents:
diff changeset
72 </tool>