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comparison msconvert_subset.xml @ 0:10f4a0356342

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author galaxyp
date Wed, 19 Dec 2012 00:10:08 -0500
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children 861e3f0c2bb6
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-1:000000000000 0:10f4a0356342
1 <tool id="msconvert_subset" name="Subset Peak List" version="0.1.0">
2 <description>against list of scan numbers or indices.</description>
3 <command interpreter="python">
4 msconvert_wrapper.py
5 --input=${input}
6 --output=${output}
7 --fromextension=${input.ext}
8 --toextension=${output_type}
9 #if $settings.settingsType == "full"
10 --binaryencoding=${settings.binary_encoding}
11 --mzencoding=${settings.mz_encoding}
12 --intensityencoding=${settings.intensity_encoding}
13 --zlib=${settings.zlib}
14 #end if
15 --filter_table="$filter.filterList"
16 #if $filter.filterType == "scan_number"
17 --filter_table_type="number"
18 #else
19 --filter_table_type="index"
20 #end if
21 </command>
22
23 <inputs>
24 <conditional name="type">
25 <param name="input_type" type="select" label="Input Type">
26 <option value="mzml">mzML</option>
27 <option value="mzxml">mzXML</option>
28 <option value="mgf">mgf</option>
29 <option value="ms2">ms2</option>
30 </param>
31 <when value="mzml">
32 <param format="mzml" name="input" type="data" label="Input mzML"/>
33 </when>
34 <when value="mzxml">
35 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
36 </when>
37 <when value="mgf">
38 <param format="mgf" name="input" type="data" label="Input mgf"/>
39 </when>
40 <when value="ms2">
41 <param format="ms2" name="input" type="data" label="Input ms2"/>
42 </when>
43 </conditional>
44 <param name="output_type" type="select" label="Output Type">
45 <option value="mzML">mzML (indexed)</option>
46 <option value="unindexed_mzML">mzML (unindexed)</option>
47 <option value="mzXML">mzXML (indexed)</option>
48 <option value="unindexed_mzXML">mzXML (unindexed)</option>
49 <option value="mgf">mgf</option>
50 <option value="ms2">ms2</option>
51 </param>
52 <conditional name="filter">
53 <param name="filterType" type="select" label="Filter by" help="">
54 <option value="scan_number" selected="true">Scan Number</option>
55 <option value="scan_index">Scan Index</option>
56 </param>
57 <when value="scan_number">
58 <param format="text" name="filterList" type="data" label="Scan Numbers"/>
59 </when>
60 <when value="scan_index">
61 <param format="text" name="filterList" type="data" label="Scan Indices"/>
62 </when>
63 </conditional>
64 <conditional name="settings">
65 <param name="settingsType" type="select" label="Advanced msconvert Settings" help="">
66 <option value="default">Use Defaults</option>
67 <option value="full">Full Parameter List</option>
68 </param>
69 <when value="default" />
70 <when value="full">
71 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
72 <option value="64" selected="true">64</option>
73 <option value="32">32</option>
74 </param>
75 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
76 <option value="64" selected="true">64</option>
77 <option value="32">32</option>
78 </param>
79 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
80 <option value="64">64</option>
81 <option value="32" selected="true">32</option>
82 </param>
83 <param type="boolean" name="zlib" label="Use zlib">
84 </param>
85 </when>
86 </conditional>
87 </inputs>
88 <outputs>
89 <data format="mzml" name="output">
90 <change_format>
91 <when input="output_type" value="mzXML" format="mzxml" />
92 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
93 <when input="output_type" value="ms2" format="ms2" />
94 <when input="output_type" value="mgf" format="mgf" />
95 </change_format>
96 </data>
97 </outputs>
98
99 <requirements>
100 <requirement type="package">proteowizard</requirement>
101 </requirements>
102
103 <help>
104 </help>
105 </tool>