annotate idxml_to_tabular.xml @ 4:1183846e70a1 draft

Uploaded
author galaxyp
date Wed, 19 Jun 2013 13:15:44 -0400
parents cf0d72c7b482
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
1 <tool id="openms_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
2 <description>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
3 Converts identification engine file formats.
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
4 </description>
2
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
5 <macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
6 <import>macros.xml</import>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
7 </macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
8 <expand macro="stdio" />
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
9 <expand macro="requires" />
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
10 <command interpreter="python">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
11 openms_wrapper.py --executable 'TextExporter' --config $config
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
12 </command>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
13 <configfiles>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
14 <configfile name="config">[simple_options]
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
15 in=${in}
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
16 out=${out}
4
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
17 $dump_type
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
18 id!first_dim_rt=$extra_rt
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
19 </configfile>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
20 </configfiles>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
21 <inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
22 <param format="idxml" name="in" type="data" label="Input Identification File"/>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
23 <param name="dump_type" type="select" label="Export type">
4
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
24 <option value="">Run, peptide, and protein information</option>
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
25 <option value="id!proteins_only=true">Run and protein information only</option>
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
26 <option value="id!peptides_only=true">Peptide information only</option>
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
27 </param>
4
1183846e70a1 Uploaded
galaxyp
parents: 2
diff changeset
28 <param name="extra_rt" type="boolean" label="Include RT information (if present)" />
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
29 </inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
30 <outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
31 <data format="tabular" name="out">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
32 </data>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
33 </outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
34 <help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
35 **What it does**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
36
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
37 Converts idXML files to tabular.
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
38
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
39 **Citation**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
40
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
41 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
42
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
43 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
44 </help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
45 </tool>