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comparison MRMMapper.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="MRMMapper" name="MRMMapper" version="1.12.0"> 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 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <macros> 4 <tool id="MRMMapper" name="MRMMapper" version="2.0.0">
5 <token name="@EXECUTABLE@">MRMMapper</token> 5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">MRMMapper</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>MRMMapper 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>MRMMapper
11 14
12 -in ${param_in} 15 #if $param_in:
13 -tr ${param_tr} 16 -in $param_in
14 -out ${param_out} 17 #end if
15 -precursor_tolerance ${param_precursor_tolerance} 18 #if $param_tr:
16 -product_tolerance ${param_product_tolerance} 19 -tr $param_tr
17 ${param_no-strict} 20 #end if
18 -threads \${GALAXY_SLOTS:-24} 21 #if $param_out:
22 -out $param_out
23 #end if
24 #if $param_precursor_tolerance:
25 -precursor_tolerance $param_precursor_tolerance
26 #end if
27 #if $param_product_tolerance:
28 -product_tolerance $param_product_tolerance
29 #end if
30 #if $param_no_strict:
31 -no-strict
32 #end if
33 -threads \${GALAXY_SLOTS:-24}
34 #if $adv_opts.adv_opts_selector=='advanced':
35 #if $adv_opts.param_force:
36 -force
37 #end if
38 #end if
19 </command> 39 </command>
20 <inputs> 40 <inputs>
21 <param name="param_in" type="data" format="mzML" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in)"/> 41 <param format="mzml" help="(-in) " label="Input file containing chromatograms (converted mzXML file)" name="param_in" optional="False" type="data"/>
22 <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/> 42 <param format="traml" help="(-tr) " label="transition file" name="param_tr" optional="False" type="data"/>
23 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance)"/> 43 <param help="(-precursor_tolerance) " label="Precursor tolerance when mapping (in Th)" name="param_precursor_tolerance" type="float" value="0.1"/>
24 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance)"/> 44 <param help="(-product_tolerance) " label="Product tolerance when mapping (in Th)" name="param_product_tolerance" type="float" value="0.1"/>
25 <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/> 45 <param checked="false" falsevalue="" help="(-no-strict) " label="run in non-strict mode and allow some chromatograms to not be mapped" name="param_no_strict" optional="True" truevalue="-no-strict" type="boolean"/>
26 </inputs> 46 <expand macro="advanced_options">
27 <outputs> 47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
28 <data name="param_out" label="Output file containing mapped chromatograms" format="mzML"/> 48 </expand>
29 </outputs> 49 </inputs>
30 <help>**What it does** 50 <outputs>
31 51 <data format="mzml" name="param_out"/>
32 MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 52 </outputs>
53 <help>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
33 54
34 55
35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html 56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html</help>
36 57 </tool>
37 @REFERENCES@
38 </help>
39 </tool>