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comparison msconvert_subset.xml @ 6:6b6bba73eadb draft

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planemo upload commit d56659dd48f8c554a832787e71aca6ae65c90848
author galaxyp
date Tue, 14 Mar 2017 16:52:39 -0400
parents ab59b1826345
children
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5:637e309295cf 6:6b6bba73eadb
1 <tool id="msconvert_subset" name="msconvert Subset Peak List" version="0.3.0">
2 <description>against list of scan numbers or indices.</description>
3 <!--
4 <requirements>
5 <requirement type="package" version="3_0_4388">proteowizard</requirement>
6 </requirements>
7 -->
8 <command interpreter="python">
9 msconvert_wrapper.py
10 --input=${input}
11 --output=${output}
12 --fromextension=${input.ext}
13 --toextension=${output_type}
14 #if $settings.settingsType == "full"
15 --binaryencoding=${settings.binary_encoding}
16 --mzencoding=${settings.mz_encoding}
17 --intensityencoding=${settings.intensity_encoding}
18 --zlib=${settings.zlib}
19 #end if
20 --filter_table="$filter.filterList"
21 #if $filter.filterType == "scan_number"
22 --filter_table_type="number"
23 #else
24 --filter_table_type="index"
25 #end if
26 </command>
27
28 <inputs>
29 <conditional name="type">
30 <param name="input_type" type="select" label="Input Type">
31 <option value="mzml">mzML</option>
32 <option value="mzxml">mzXML</option>
33 <option value="mgf">mgf</option>
34 <option value="ms2">ms2</option>
35 </param>
36 <when value="mzml">
37 <param format="mzml" name="input" type="data" label="Input mzML"/>
38 </when>
39 <when value="mzxml">
40 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
41 </when>
42 <when value="mgf">
43 <param format="mgf" name="input" type="data" label="Input mgf"/>
44 </when>
45 <when value="ms2">
46 <param format="ms2" name="input" type="data" label="Input ms2"/>
47 </when>
48 </conditional>
49 <param name="output_type" type="select" label="Output Type">
50 <option value="mzML">mzML (indexed)</option>
51 <option value="unindexed_mzML">mzML (unindexed)</option>
52 <option value="mzXML">mzXML (indexed)</option>
53 <option value="unindexed_mzXML">mzXML (unindexed)</option>
54 <option value="mgf">mgf</option>
55 <option value="ms2">ms2</option>
56 </param>
57 <conditional name="filter">
58 <param name="filterType" type="select" label="Filter by" help="">
59 <option value="scan_number" selected="true">Scan Number</option>
60 <option value="scan_index">Scan Index</option>
61 </param>
62 <when value="scan_number">
63 <param format="text" name="filterList" type="data" label="Scan Numbers"/>
64 </when>
65 <when value="scan_index">
66 <param format="text" name="filterList" type="data" label="Scan Indices"/>
67 </when>
68 </conditional>
69 <conditional name="settings">
70 <param name="settingsType" type="select" label="Advanced msconvert Settings" help="">
71 <option value="default">Use Defaults</option>
72 <option value="full">Full Parameter List</option>
73 </param>
74 <when value="default" />
75 <when value="full">
76 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
77 <option value="64" selected="true">64</option>
78 <option value="32">32</option>
79 </param>
80 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
81 <option value="64" selected="true">64</option>
82 <option value="32">32</option>
83 </param>
84 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
85 <option value="64">64</option>
86 <option value="32" selected="true">32</option>
87 </param>
88 <param type="boolean" name="zlib" label="Use zlib">
89 </param>
90 </when>
91 </conditional>
92 </inputs>
93 <outputs>
94 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" >
95 <change_format>
96 <when input="output_type" value="mzXML" format="mzxml" />
97 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
98 <when input="output_type" value="ms2" format="ms2" />
99 <when input="output_type" value="mgf" format="mgf" />
100 </change_format>
101 </data>
102 </outputs>
103 <help>
104 </help>
105 </tool>