Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher

comparison OpenSwathMzMLFileCacher.xml @ 1:22820a211fe8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:47:55 -0400
parents 5a7e590eb955
children e1c2ee148254
comparison
equal deleted inserted replaced
0:5a7e590eb955 1:22820a211fe8
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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: []--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.1.0"> 4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.2.0">
5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> 5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> 7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
16 -in $param_in 16 -in $param_in
17 #end if 17 #end if
18 #if $param_out: 18 #if $param_out:
19 -out $param_out 19 -out $param_out
20 #end if 20 #end if
21 #if $param_out_type:
22 -out_type
23 #if " " in str($param_out_type):
24 "$param_out_type"
25 #else
26 $param_out_type
27 #end if
28 #end if
21 #if $param_convert_back: 29 #if $param_convert_back:
22 -convert_back 30 -convert_back
23 #end if 31 #end if
24 #if $adv_opts.adv_opts_selector=='advanced': 32 #if $adv_opts.adv_opts_selector=='advanced':
25 #if $adv_opts.param_force: 33 #if $adv_opts.param_force:
26 -force 34 -force
27 #end if 35 #end if
28 #end if 36 #end if
29 </command> 37 </command>
30 <inputs> 38 <inputs>
31 <param name="param_in" type="data" format="mzml" optional="False" label="transition file ('csv')" help="(-in) "/> 39 <param name="param_in" type="data" format="mzml,sqMass" optional="False" label="Input mzML file" help="(-in) "/>
40 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
41 <option value="mzML">mzML</option>
42 <option value="sqMass">sqMass</option>
43 </param>
32 <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/> 44 <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/>
33 <expand macro="advanced_options"> 45 <expand macro="advanced_options">
34 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
35 </expand> 47 </expand>
36 </inputs> 48 </inputs>
37 <outputs> 49 <outputs>
38 <data name="param_out" format="data"/> 50 <data name="param_out" format="mzml"/>
39 </outputs> 51 </outputs>
40 <help>This tool caches the spectra and chromatogram data of an mzML to disk. 52 <help>This tool caches the spectra and chromatogram data of an mzML to disk.
41 53
42 54
43 For more information, visit </help> 55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathMzMLFileCacher.html</help>
44 </tool> 56 </tool>