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comparison msconvert3.xml @ 5:08bb52273ae1

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Bjoern: remove unused repository dependency, cleanups
author Jim Johnson <jj@umn.edu>
date Mon, 17 Feb 2014 08:13:33 -0600
parents 001e77708ec9
children
comparison
equal deleted inserted replaced
4:001e77708ec9 5:08bb52273ae1
1 <tool id="msconvert3" name="msconvert3" version="0.2.0"> 1 <tool id="msconvert3" name="msconvert3" version="0.2.1">
2 <!-- BEGIN_VERSION_DEFAULT --> 2 <!-- BEGIN_VERSION_DEFAULT -->
3 <description>Convert and filter a mass spec peak list</description> 3 <description>Convert and filter a mass spec peak list</description>
4 <!-- END_VERSION_DEFAULT --> 4 <!-- END_VERSION_DEFAULT -->
5 5 <requirements>
6 <requirement type="package">proteowizard</requirement>
7 </requirements>
6 <command interpreter="python"> 8 <command interpreter="python">
7 #set $ext = $input.ext 9 #set $ext = $input.ext
8 #if $ext.startswith("m:") 10 #if $ext.startswith("m:")
9 #set $ext = $ext[len("m:"):] 11 #set $ext = $ext[len("m:"):]
10 #end if 12 #end if
12 --input=${input} 14 --input=${input}
13 #if hasattr($input, 'display_name') 15 #if hasattr($input, 'display_name')
14 --input_name='${input.display_name}' 16 --input_name='${input.display_name}'
15 #end if 17 #end if
16 --output=${output} 18 --output=${output}
17 ## BEGIN_VERSION_DEFAULT 19 ## BEGIN_VERSION_DEFAULT
18 --fromextension=$ext 20 --fromextension=$ext
19 ## END_VERSION_DEFAULT 21 ## END_VERSION_DEFAULT
20 22
21 23
22 --toextension=${output_type} 24 --toextension=${output_type}
114 116
115 <inputs> 117 <inputs>
116 118
117 <!-- BEGIN_VERSION_DEFAULT --> 119 <!-- BEGIN_VERSION_DEFAULT -->
118 <conditional name="type"> 120 <conditional name="type">
119 <param name="input_type" type="select" label="Input Type" help="select file type of input data from history- mzml, mzXML, mgf or ms2. then select appropriate input file from drop down menu depending on input in history"> 121 <param name="input_type" type="select" label="Input Type">
120 <option value="mzml">mzML</option> 122 <option value="mzml">mzML</option>
121 <option value="mzxml">mzXML</option> 123 <option value="mzxml">mzXML</option>
122 <option value="mgf">mgf</option> 124 <option value="mgf">mgf</option>
123 <option value="ms2">ms2</option> 125 <option value="ms2">ms2</option>
124 </param> 126 </param>
134 <when value="ms2"> 136 <when value="ms2">
135 <param format="ms2" name="input" type="data" label="Input ms2"/> 137 <param format="ms2" name="input" type="data" label="Input ms2"/>
136 </when> 138 </when>
137 </conditional> 139 </conditional>
138 <!-- END_VERSION_DEFAULT --> 140 <!-- END_VERSION_DEFAULT -->
139 <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is The standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)."> 141 <param name="output_type" type="select" label="Output Type">
140 <option value="mzML">mzML (indexed)</option> 142 <option value="mzML">mzML (indexed)</option>
141 <option value="unindexed_mzML">mzML (unindexed)</option> 143 <option value="unindexed_mzML">mzML (unindexed)</option>
142 <option value="mzXML">mzXML (indexed)</option> 144 <option value="mzXML">mzXML (indexed)</option>
143 <option value="unindexed_mzXML">mzXML (unindexed)</option> 145 <option value="unindexed_mzXML">mzXML (unindexed)</option>
144 <option value="mgf">mgf</option> 146 <option value="mgf">mgf</option>
145 <option value="ms2">ms2</option> 147 <option value="ms2">ms2</option>
146 </param> 148 </param>
147 <conditional name="filtering"> 149 <conditional name="filtering">
148 <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (see also peaklist processing)" /> 150 <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" />
149 <when value="false" /> 151 <when value="false" />
150 <when value="true"> 152 <when value="true">
151 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> 153 <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" />
152 <!-- BEGIN_VERSION_3 --> 154 <!-- BEGIN_VERSION_3 -->
153 <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> 155 <param type="boolean" name="precursor_refine" label="Refine Precursor?" />
353 <when input="output_type" value="ms2" format="ms2" /> 355 <when input="output_type" value="ms2" format="ms2" />
354 <when input="output_type" value="mgf" format="mgf" /> 356 <when input="output_type" value="mgf" format="mgf" />
355 </change_format> 357 </change_format>
356 </data> 358 </data>
357 </outputs> 359 </outputs>
358
359 <requirements>
360 <requirement type="package">proteowizard</requirement>
361 </requirements>
362
363 <help> 360 <help>
364 **What it does** 361 **What it does**
365 362
366 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available. 363 Allows interconversion within various mass spectrometry peak list formats. Additional options such as filtering and/or precursor recalculation are available.
367 364