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comparison DTAExtractor.xml @ 0:5f34a3bd4f2f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 10:21:15 -0500
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-1:000000000000 0:5f34a3bd4f2f
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="DTAExtractor" name="DTAExtractor" version="2.1.0">
5 <description>Extracts spectra of an MS run file to several files in DTA format.</description>
6 <macros>
7 <token name="@EXECUTABLE@">DTAExtractor</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>DTAExtractor
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out "$param_out"
20 #end if
21 #if $param_mz:
22 -mz "$param_mz"
23 #end if
24 #if $param_rt:
25 -rt "$param_rt"
26 #end if
27 #if $param_level:
28 -level "$param_level"
29 #end if
30 #if $adv_opts.adv_opts_selector=='advanced':
31 #if $adv_opts.param_force:
32 -force
33 #end if
34 #end if
35 &gt; $param_stdout
36 </command>
37 <inputs>
38 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
39 <param name="param_out" type="text" size="30" label="base name of DTA output files (RT, m/z and extension are appended)" help="(-out) ">
40 <sanitizer>
41 <valid initial="string.printable">
42 <remove value="'"/>
43 <remove value="&quot;"/>
44 </valid>
45 </sanitizer>
46 </param>
47 <param name="param_mz" type="text" size="30" value=":" label="m/z range of precursor peaks to extract" help="(-mz) &lt;br&gt;This option is ignored for MS level 1">
48 <sanitizer>
49 <valid initial="string.printable">
50 <remove value="'"/>
51 <remove value="&quot;"/>
52 </valid>
53 </sanitizer>
54 </param>
55 <param name="param_rt" type="text" size="30" value=":" label="retention time range of spectra to extract" help="(-rt) ">
56 <sanitizer>
57 <valid initial="string.printable">
58 <remove value="'"/>
59 <remove value="&quot;"/>
60 </valid>
61 </sanitizer>
62 </param>
63 <param name="param_level" type="text" size="30" value="1,2,3" label="MS levels to extract" help="(-level) ">
64 <sanitizer>
65 <valid initial="string.printable">
66 <remove value="'"/>
67 <remove value="&quot;"/>
68 </valid>
69 </sanitizer>
70 </param>
71 <expand macro="advanced_options">
72 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
73 </expand>
74 </inputs>
75 <outputs>
76 <data name="param_stdout" format="text" label="Output from stdout"/>
77 </outputs>
78 <help>Extracts spectra of an MS run file to several files in DTA format.
79
80
81 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_DTAExtractor.html</help>
82 </tool>