Mercurial > repos > pravs > msms_extractor
comparison MSMS_Extractor.xml @ 2:aa944e3a353c draft
planemo upload
author | pravs |
---|---|
date | Thu, 03 Aug 2017 13:53:09 -0400 |
parents | f444e529363d |
children | e7c63cfef363 |
comparison
equal
deleted
inserted
replaced
1:f444e529363d | 2:aa944e3a353c |
---|---|
1 | 1 |
2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.0.0"> | 2 <tool id="MSMS_Extractor" name="MSMS_Extractor" version="1.1.0"> |
3 <description>Removes scans with identified PSMs from the mzML file(s).</description> | 3 <description>Extract scans based on PSM report from the mzML file(s).</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="3.0.9016">proteowizard</requirement> | 5 <requirement type="package" version="3.0.9016">proteowizard</requirement> |
6 <requirement type="package" version="3.4">pyteomics</requirement> | 6 <requirement type="package" version="3.4">pyteomics</requirement> |
7 </requirements> | 7 </requirements> |
8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]}]]></command> | 8 <command interpreter="python"><![CDATA[MSMS_Extractor.py $spectrumfile $psmreportfile $output ${spectrumfile.name.rsplit('.',1)[0]} $removeretain.doremoveretain $removeretain.num_random_scans]]></command> |
9 <inputs> | 9 <inputs> |
10 <param name="spectrumfile" type="data" format="mzml"> | 10 <param name="spectrumfile" type="data" format="mzml"> |
11 <label>Input mzML File</label> | 11 <label>Input mzML File</label> |
12 </param> | 12 </param> |
13 <param name="psmreportfile" type="data" format="tabular"> | 13 <param name="psmreportfile" type="data" format="tabular"> |
14 <label>Input PSM Report File</label> | 14 <label>Input PSM Report File</label> |
15 </param> | 15 </param> |
16 | |
17 <conditional name="removeretain"> | |
18 <param name="doremoveretain" type="boolean" truevalue="retain" falsevalue="remove" label="Remove or Retain the given Scans" help="Retain=Yes; Remove=No (default)" /> | |
19 <when value="remove"> | |
20 <param name="num_random_scans" type="hidden" value="0" /> | |
21 </when> | |
22 <when value="retain"> | |
23 <param name="num_random_scans" type="integer" label="Add N random scans in addition to those in the list" value="0" optional="false" /> | |
24 </when> | |
25 </conditional> | |
26 | |
16 </inputs> | 27 </inputs> |
17 | 28 |
18 <outputs> | 29 <outputs> |
19 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" /> | 30 <data format="mzml" name="output" label="${spectrumfile.name.rsplit('.',1)[0]}.mzml" /> |
20 </outputs> | 31 </outputs> |
21 | 32 |
22 | 33 |
23 <help> | 34 <help> |
24 MSMS_Extractor reads scan numbers from the PSM report (scan numbers with identified PSM) and removes it from the mzML file. | 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. |
36 | |
37 Remove option: | |
38 Creates a new mzml file with all the unidentified scans (removes those that are in the PSM report). | |
39 | |
40 Retain option: | |
41 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. | |
42 | |
43 | |
44 Please Note: This tool currently works only with PeptideShaker generated PSM report file. | |
45 | |
25 </help> | 46 </help> |
26 </tool> | 47 </tool> |