annotate idxml_to_peptides.xml @ 3:8fa16707e162 draft

Update.
author galaxyp
date Fri, 10 May 2013 17:31:59 -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_peptides" version="0.1.0" name="Export peptide report from idXML ">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
2 <description>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
3 </description>
2
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
4 <macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
5 <import>macros.xml</import>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
6 </macros>
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
7 <expand macro="stdio" />
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
8 <expand macro="requires" />
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
9 <command interpreter="python">
2
cf0d72c7b482 Update.
galaxyp
parents: 0
diff changeset
10 openms_exporter.py --type peptide --in ${in} --out ${out}
0
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
11 </command>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
12 <inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
13 <param format="idxml" name="in" type="data" label="Input Identification File"/>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
14 </inputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
15 <outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
16 <data format="tabular" name="out">
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
17 </data>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
18 </outputs>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
19 <help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
20 **What it does**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
21
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
22 Extracts a peptide-level tabular report from an idXML file. The "Export idXML to Tabular" tool provides similar functionality and wraps the OpenMS program TextExporter. However the output of that program may be difficult to utilize in Galaxy and it fails under under certain conditions (e.g. on idXML files coming from PepNovo). This tool was designed for Galaxy and its output is easier to process with other tools in Galaxy.
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
23
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
24 **Citation**
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
25
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
26 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
27 </help>
ba86fd127f5a Uploaded
galaxyp
parents:
diff changeset
28 </tool>