annotate mzml_to_mgf.xml @ 2:418f42b34049 draft

Reuploading
author iracooke
date Mon, 23 Jul 2012 00:20:58 -0400
parents a929e27eb203
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
1 <tool id="mzml_to_mgf_1" name="MzML to mgf" version="1.0.0">
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
2 <requirements>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
3 <requirement type="package">protk</requirement>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
4 </requirements>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
5
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
6 <description>Converts an mzML file to mgf suitable for searching by omssa</description>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
7
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
8 <command>file_convert.rb $input_file -o $output $maldi</command>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
9
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
10 <inputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
11
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
12 <param name="input_file" type="data" format="mzml" multiple="false" label="Input File" help="Line Spectra in mzML format"/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
13 <param name="maldi" type="boolean" label="Is the data from a MALDI instrument" truevalue="-l" falsevalue=""/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
14
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
15 </inputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
16
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
17 <outputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
18 <data format="mgf" name="output" metadata_source="input_file" label="${input_file.display_name}.mgf" from_work_dir="converted.mgf"/>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
19 </outputs>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
20
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
21 <help>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
22 Convert line spectra to Mascot Generic Format
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
23 </help>
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
24
a929e27eb203 Uploaded
iracooke
parents:
diff changeset
25 </tool>