Mercurial > repos > galaxyp > msconvert
annotate msconvert_subset.xml @ 9:dd4ba10d0c45 draft
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author | galaxyp |
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date | Wed, 07 Dec 2016 16:43:07 -0500 |
parents | d2c61663e33c |
children |
rev | line source |
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8 | 1 <tool id="msconvert_subset" name="msconvert Subset Peak List" version="0.3.0"> |
7 | 2 <description>against list of scan numbers or indices.</description> |
8 | 3 <!-- |
7 | 4 <requirements> |
8 | 5 <requirement type="package" version="3_0_4388">proteowizard</requirement> |
7 | 6 </requirements> |
8 | 7 --> |
7 | 8 <command interpreter="python"> |
8 | 9 msconvert_wrapper.py |
10 --input=${input} | |
11 --output=${output} | |
12 --fromextension=${input.ext} | |
13 --toextension=${output_type} | |
7 | 14 #if $settings.settingsType == "full" |
8 | 15 --binaryencoding=${settings.binary_encoding} |
16 --mzencoding=${settings.mz_encoding} | |
7 | 17 --intensityencoding=${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> | |
8 | 52 <option value="mzXML">mzXML (indexed)</option> |
7 | 53 <option value="unindexed_mzXML">mzXML (unindexed)</option> |
54 <option value="mgf">mgf</option> | |
8 | 55 <option value="ms2">ms2</option> |
7 | 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> | |
8 | 61 </param> |
7 | 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> | |
8 | 88 <param type="boolean" name="zlib" label="Use zlib"> |
7 | 89 </param> |
90 </when> | |
91 </conditional> | |
92 </inputs> | |
93 <outputs> | |
9
dd4ba10d0c45
planemo upload commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
8
diff
changeset
|
94 <data format="mzml" name="output" label="${type.input.name.rsplit('.',1)[0]}.${output_type}" > |
7 | 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> |