Mercurial > repos > galaxyp > openms_fileconverter

comparison FileConverter.xml @ 7:1fe84d73c19c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:06:03 -0500
parents ed6890cfc90a
children 1a186cc82c8d
comparison
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6:406855426f41 7:1fe84d73c19c
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 CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileConverter" name="FileConverter" version="2.2.0"> 4 <tool id="FileConverter" name="FileConverter" version="2.3.0">
5 <description>Converts between different MS file formats.</description> 5 <description>Converts between different MS file formats.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileConverter</token> 7 <token name="@EXECUTABLE@">FileConverter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
41 #if $adv_opts.param_MGF_compact: 41 #if $adv_opts.param_MGF_compact:
42 -MGF_compact 42 -MGF_compact
43 #end if 43 #end if
44 #if $adv_opts.param_force_MaxQuant_compatibility: 44 #if $adv_opts.param_force_MaxQuant_compatibility:
45 -force_MaxQuant_compatibility 45 -force_MaxQuant_compatibility
46 #end if
47 #if $adv_opts.param_force_TPP_compatibility:
48 -force_TPP_compatibility
46 #end if 49 #end if
47 #if $adv_opts.param_write_scan_index: 50 #if $adv_opts.param_write_scan_index:
48 -write_scan_index 51 -write_scan_index
49 #if " " in str($adv_opts.param_write_scan_index): 52 #if " " in str($adv_opts.param_write_scan_index):
50 "$adv_opts.param_write_scan_index" 53 "$adv_opts.param_write_scan_index"
87 <option value="csv">csv</option> 90 <option value="csv">csv</option>
88 </param> 91 </param>
89 <param name="param_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/> 92 <param name="param_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/>
90 <param name="param_MGF_compact" display="radio" type="boolean" truevalue="-MGF_compact" falsevalue="" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact) "/> 93 <param name="param_MGF_compact" display="radio" type="boolean" truevalue="-MGF_compact" falsevalue="" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact) "/>
91 <param name="param_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/> 94 <param name="param_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
95 <param name="param_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_compatibility) "/>
92 <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it"> 96 <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
93 <option value="true" selected="true">true</option> 97 <option value="true" selected="true">true</option>
94 <option value="false">false</option> 98 <option value="false">false</option>
95 </param> 99 </param>
96 <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/> 100 <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/>