annotate selectproteinids.xml @ 1:f3fa21cda5f5 draft default tip

planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
author labis-app
date Fri, 10 Aug 2018 15:45:44 -0400
parents ba070efb6f78
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
1 <?xml version="1.0"?>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
2 <tool id="selectproteinids" name="Filter ids" version="1.0" hidden="false">
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
3
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
4 <description></description>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
5 <command interpreter="perl">
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
6 selectproteinids.pl $input $maintaincon $out_file
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
7 </command>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
8
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
9 <inputs>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
10 <param format="tabular" name="input" type="data" label="Input table"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
11
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
12 <param name="maintaincon" type="select" display="radio" label="Maintain contaminants">
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
13 <option value="yes">Yes</option>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
14 <option value="no">No</option>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
15 </param>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
16
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
17 </inputs>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
18
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
19 <outputs>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
20 <data format="tabular" name="out_file" label="${input.name} filtered"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
21 </outputs>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
22
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
23 <tests>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
24 <test>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
25 <param name="input" value="protein_ids_simple.csv"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
26 <param name="maintaincon" value="yes"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
27 <output name="out_file" file="proteinGroups_csv_filtered_with_contaminants.tabular"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
28 </test>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
29
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
30 <test>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
31 <param name="input" value="protein_ids_simple.csv"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
32 <param name="maintaincon" value="no"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
33 <output name="out_file" file="proteinGroups_csv_filtered_without_contaminants.tabular"/>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
34 </test>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
35
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
36 </tests>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
37
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
38 <help>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
39
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
40 Input: Protein Groups from MaxQuant
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
41
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
42
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
43 Output: Table with id's got from MaxQuant Protein Groups
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
44
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
45 </help>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
46
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
47 <citations>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
48 <citation type="bibtex">
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
49 @misc{Concatenate,
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
50 author = {Application, Labis},
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
51 year = 2018,
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
52 title = Concatenate,
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
53 publisher = labisapplications
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
54 }
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
55 </citation>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
56 </citations>
ba070efb6f78 planemo upload commit 13e72e84c523bda22bda792bbebf4720d28542d5-dirty
labis-app
parents:
diff changeset
57 </tool>