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comparison msconvert.xml @ 9:dd4ba10d0c45 draft

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planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:43:07 -0500
parents d2c61663e33c
children 9d5de24e6ef7
comparison
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8:d2c61663e33c 9:dd4ba10d0c45
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3_0_4388">proteowizard</requirement> 7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
8 </requirements> 8 </requirements>
9 --> 9 -->
10 <command interpreter="python"> 10 <command interpreter="python">
11 #import re
11 #set $ext = $input.ext 12 #set $ext = $input.ext
12 msconvert_wrapper.py 13 msconvert_wrapper.py
13 --input=${input} 14 #if $type.input_type == 'wiff':
14 #if hasattr($input, 'display_name') 15 #set basename = 'absciex'
15 --input_name='${input.display_name}' 16 #if hasattr($input, 'display_name')
17 #set basename = $re.sub('\W','_',$input.display_name)
18 #end if
19 --input=${input.extra_files_path}/wiff
20 --input_name='${basename}.wiff
21 --implicit=${input.extra_files_path}/wiff_scan
22 --input=${input.extra_files_path}/wiff_scan
23 --input_name='${basename}.wiff.scan
24 #else
25 --input=${input}
26 #if hasattr($input, 'display_name')
27 --input_name='${input.display_name}'
28 #end if
16 #end if 29 #end if
17 --output=${output} 30 --output=${output}
18 ## BEGIN_VERSION_DEFAULT 31 ## BEGIN_VERSION_DEFAULT
19 --fromextension=$ext 32 --fromextension=$ext
20 ## END_VERSION_DEFAULT 33 ## END_VERSION_DEFAULT
120 <param name="input_type" type="select" label="Input Type"> 133 <param name="input_type" type="select" label="Input Type">
121 <option value="mzml">mzML</option> 134 <option value="mzml">mzML</option>
122 <option value="mzxml">mzXML</option> 135 <option value="mzxml">mzXML</option>
123 <option value="mgf">mgf</option> 136 <option value="mgf">mgf</option>
124 <option value="ms2">ms2</option> 137 <option value="ms2">ms2</option>
138 <option value="wiff">wiff</option>
125 </param> 139 </param>
126 <when value="mzml"> 140 <when value="mzml">
127 <param format="mzml" name="input" type="data" label="Input mzML"/> 141 <param format="mzml" name="input" type="data" label="Input mzML"/>
128 </when> 142 </when>
129 <when value="mzxml"> 143 <when value="mzxml">
132 <when value="mgf"> 146 <when value="mgf">
133 <param format="mgf" name="input" type="data" label="Input mgf"/> 147 <param format="mgf" name="input" type="data" label="Input mgf"/>
134 </when> 148 </when>
135 <when value="ms2"> 149 <when value="ms2">
136 <param format="ms2" name="input" type="data" label="Input ms2"/> 150 <param format="ms2" name="input" type="data" label="Input ms2"/>
151 </when>
152 <when value="wiff">
153 <param format="wiff" name="input" type="data" label="Input wiff"/>
137 </when> 154 </when>
138 </conditional> 155 </conditional>
139 <!-- END_VERSION_DEFAULT --> 156 <!-- END_VERSION_DEFAULT -->
140 <param name="output_type" type="select" label="Output Type"> 157 <param name="output_type" type="select" label="Output Type">
141 <option value="mzML">mzML (indexed)</option> 158 <option value="mzML">mzML (indexed)</option>
345 </conditional> 362 </conditional>
346 363
347 364
348 </inputs> 365 </inputs>
349 <outputs> 366 <outputs>
350 <data format="mzml" name="output"> 367 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
351 <change_format> 368 <change_format>
352 <when input="output_type" value="mzXML" format="mzxml" /> 369 <when input="output_type" value="mzXML" format="mzxml" />
353 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> 370 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
354 <when input="output_type" value="ms2" format="ms2" /> 371 <when input="output_type" value="ms2" format="ms2" />
355 <when input="output_type" value="mgf" format="mgf" /> 372 <when input="output_type" value="mgf" format="mgf" />