Mercurial > repos > galaxyp > openms_mrmmapper

comparison MRMMapper.xml @ 5:f74d3da5abd2 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 12:53:22 -0500
parents 129e682a554c
children 305bf5edf3ce
comparison
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4:a6ae8429e318 5:f74d3da5abd2
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="MRMMapper" name="MRMMapper" version="2.2.0"> 4 <tool id="MRMMapper" name="MRMMapper" version="2.3.0">
5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description> 5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MRMMapper</token> 7 <token name="@EXECUTABLE@">MRMMapper</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
28 -product_tolerance $param_product_tolerance 28 -product_tolerance $param_product_tolerance
29 #end if 29 #end if
30 #if $param_no_strict: 30 #if $param_no_strict:
31 -no-strict 31 -no-strict
32 #end if 32 #end if
33 #if $param_allow_multiple_mappings:
34 -allow_multiple_mappings
35 #end if
33 #if $adv_opts.adv_opts_selector=='advanced': 36 #if $adv_opts.adv_opts_selector=='advanced':
34 #if $adv_opts.param_force: 37 #if $adv_opts.param_force:
35 -force 38 -force
36 #end if 39 #end if
37 #end if 40 #end if
40 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/> 43 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/>
41 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/> 44 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
42 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/> 45 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
43 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/> 46 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>
44 <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/> 47 <param name="param_no_strict" display="radio" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
48 <param name="param_allow_multiple_mappings" display="radio" type="boolean" truevalue="-allow_multiple_mappings" falsevalue="" checked="false" optional="True" label="Allow multiple mappings (will take the last matching from the TraML)" help="(-allow_multiple_mappings) "/>
45 <expand macro="advanced_options"> 49 <expand macro="advanced_options">
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 50 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
47 </expand> 51 </expand>
48 </inputs> 52 </inputs>
49 <outputs> 53 <outputs>