annotate MSMS_Extractor.xml @ 5:c2f8e3164537 draft

planemo upload
author pravs
date Thu, 03 Aug 2017 18:17:59 -0400
parents 59654a11787e
children 2c3e2509e9bc
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
093015b1b904 planemo upload
pravs
parents:
diff changeset
1
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.1.0">
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
3 <description>Extract scans based on PSM report from the mzML file(s).</description>
0
093015b1b904 planemo upload
pravs
parents:
diff changeset
4 <requirements>
093015b1b904 planemo upload
pravs
parents:
diff changeset
5 <requirement type="package" version="3.0.9016">proteowizard</requirement>
093015b1b904 planemo upload
pravs
parents:
diff changeset
6 <requirement type="package" version="3.4">pyteomics</requirement>
093015b1b904 planemo upload
pravs
parents:
diff changeset
7 </requirements>
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]} $removeretain.doremoveretain $removeretain.num_random_scans]]></command>
0
093015b1b904 planemo upload
pravs
parents:
diff changeset
9 <inputs>
093015b1b904 planemo upload
pravs
parents:
diff changeset
10 <param name="spectrumfile" type="data" format="mzml">
093015b1b904 planemo upload
pravs
parents:
diff changeset
11 <label>Input mzML File</label>
093015b1b904 planemo upload
pravs
parents:
diff changeset
12 </param>
093015b1b904 planemo upload
pravs
parents:
diff changeset
13 <param name="psmreportfile" type="data" format="tabular">
093015b1b904 planemo upload
pravs
parents:
diff changeset
14 <label>Input PSM Report File</label>
093015b1b904 planemo upload
pravs
parents:
diff changeset
15 </param>
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
16
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
17 <conditional name="removeretain">
3
e7c63cfef363 planemo upload
pravs
parents: 2
diff changeset
18 <param name="doremoveretain" type="boolean" truevalue="retain" falsevalue="remove" label="Retain or Remove the given Scans" help="Retain=Yes; Remove=No (default)" />
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
19 <when value="remove">
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
20 <param name="num_random_scans" type="hidden" value="0" />
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
21 </when>
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
22 <when value="retain">
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
23 <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="false" />
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
24 </when>
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
25 </conditional>
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
26
0
093015b1b904 planemo upload
pravs
parents:
diff changeset
27 </inputs>
093015b1b904 planemo upload
pravs
parents:
diff changeset
28
093015b1b904 planemo upload
pravs
parents:
diff changeset
29 <outputs>
093015b1b904 planemo upload
pravs
parents:
diff changeset
30 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" />
093015b1b904 planemo upload
pravs
parents:
diff changeset
31 </outputs>
093015b1b904 planemo upload
pravs
parents:
diff changeset
32
093015b1b904 planemo upload
pravs
parents:
diff changeset
33
093015b1b904 planemo upload
pravs
parents:
diff changeset
34 <help>
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
35 MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and gives option to create a new mzml file, either with those scans or without those scans.
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
36
4
59654a11787e planemo upload
pravs
parents: 3
diff changeset
37 ----
59654a11787e planemo upload
pravs
parents: 3
diff changeset
38
59654a11787e planemo upload
pravs
parents: 3
diff changeset
39 REMOVE option:
59654a11787e planemo upload
pravs
parents: 3
diff changeset
40
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
41 Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report).
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
42
4
59654a11787e planemo upload
pravs
parents: 3
diff changeset
43
59654a11787e planemo upload
pravs
parents: 3
diff changeset
44 RETAIN option:
59654a11787e planemo upload
pravs
parents: 3
diff changeset
45
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
46 Creates a new mzml file with only those scans that is present in the PSM report. In addition to this, it also has an option to add N number of randomly selected scans to the output mzml file.
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
47
4
59654a11787e planemo upload
pravs
parents: 3
diff changeset
48 ----
2
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
49
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
50 Please Note: This tool currently works only with PeptideShaker generated PSM report file.
aa944e3a353c planemo upload
pravs
parents: 1
diff changeset
51
0
093015b1b904 planemo upload
pravs
parents:
diff changeset
52 </help>
093015b1b904 planemo upload
pravs
parents:
diff changeset
53 </tool>