Mercurial > repos > galaxyp > msconvert
annotate msconvert_subset.xml @ 5:08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 17 Feb 2014 08:13:33 -0600 |
parents | 861e3f0c2bb6 |
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rev | line source |
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08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
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changeset
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1 <tool id="msconvert_subset" name="Subset Peak List" version="0.2.1"> |
0 | 2 <description>against list of scan numbers or indices.</description> |
5
08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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3 <requirements> |
08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
4 <requirement type="package">proteowizard</requirement> |
08bb52273ae1
Bjoern: remove unused repository dependency, cleanups
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
5 </requirements> |
0 | 6 <command interpreter="python"> |
7 msconvert_wrapper.py | |
8 --input=${input} | |
9 --output=${output} | |
10 --fromextension=${input.ext} | |
11 --toextension=${output_type} | |
12 #if $settings.settingsType == "full" | |
13 --binaryencoding=${settings.binary_encoding} | |
14 --mzencoding=${settings.mz_encoding} | |
15 --intensityencoding=${settings.intensity_encoding} | |
16 --zlib=${settings.zlib} | |
17 #end if | |
18 --filter_table="$filter.filterList" | |
19 #if $filter.filterType == "scan_number" | |
20 --filter_table_type="number" | |
21 #else | |
22 --filter_table_type="index" | |
23 #end if | |
24 </command> | |
25 | |
26 <inputs> | |
27 <conditional name="type"> | |
28 <param name="input_type" type="select" label="Input Type"> | |
29 <option value="mzml">mzML</option> | |
30 <option value="mzxml">mzXML</option> | |
31 <option value="mgf">mgf</option> | |
32 <option value="ms2">ms2</option> | |
33 </param> | |
34 <when value="mzml"> | |
35 <param format="mzml" name="input" type="data" label="Input mzML"/> | |
36 </when> | |
37 <when value="mzxml"> | |
38 <param format="mzxml" name="input" type="data" label="Input mzXML"/> | |
39 </when> | |
40 <when value="mgf"> | |
41 <param format="mgf" name="input" type="data" label="Input mgf"/> | |
42 </when> | |
43 <when value="ms2"> | |
44 <param format="ms2" name="input" type="data" label="Input ms2"/> | |
45 </when> | |
46 </conditional> | |
47 <param name="output_type" type="select" label="Output Type"> | |
48 <option value="mzML">mzML (indexed)</option> | |
49 <option value="unindexed_mzML">mzML (unindexed)</option> | |
50 <option value="mzXML">mzXML (indexed)</option> | |
51 <option value="unindexed_mzXML">mzXML (unindexed)</option> | |
52 <option value="mgf">mgf</option> | |
53 <option value="ms2">ms2</option> | |
54 </param> | |
55 <conditional name="filter"> | |
56 <param name="filterType" type="select" label="Filter by" help=""> | |
57 <option value="scan_number" selected="true">Scan Number</option> | |
58 <option value="scan_index">Scan Index</option> | |
59 </param> | |
60 <when value="scan_number"> | |
61 <param format="text" name="filterList" type="data" label="Scan Numbers"/> | |
62 </when> | |
63 <when value="scan_index"> | |
64 <param format="text" name="filterList" type="data" label="Scan Indices"/> | |
65 </when> | |
66 </conditional> | |
67 <conditional name="settings"> | |
68 <param name="settingsType" type="select" label="Advanced msconvert Settings" help=""> | |
69 <option value="default">Use Defaults</option> | |
70 <option value="full">Full Parameter List</option> | |
71 </param> | |
72 <when value="default" /> | |
73 <when value="full"> | |
74 <param type="select" name="binary_encoding" label="Binary Encoding Precision"> | |
75 <option value="64" selected="true">64</option> | |
76 <option value="32">32</option> | |
77 </param> | |
78 <param type="select" name="mz_encoding" label="m/z Encoding Precision"> | |
79 <option value="64" selected="true">64</option> | |
80 <option value="32">32</option> | |
81 </param> | |
82 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> | |
83 <option value="64">64</option> | |
84 <option value="32" selected="true">32</option> | |
85 </param> | |
86 <param type="boolean" name="zlib" label="Use zlib"> | |
87 </param> | |
88 </when> | |
89 </conditional> | |
90 </inputs> | |
91 <outputs> | |
92 <data format="mzml" name="output"> | |
93 <change_format> | |
94 <when input="output_type" value="mzXML" format="mzxml" /> | |
95 <when input="output_type" value="unindexed_mzXML" format="mzxml" /> | |
96 <when input="output_type" value="ms2" format="ms2" /> | |
97 <when input="output_type" value="mgf" format="mgf" /> | |
98 </change_format> | |
99 </data> | |
100 </outputs> | |
101 <help> | |
102 </help> | |
103 </tool> |