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comparison MRMMapper.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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-1:000000000000 0:3d84209d3178
1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="MRMMapper" name="MRMMapper" version="1.12.0">
3 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
4 <macros>
5 <token name="@EXECUTABLE@">MRMMapper</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>MRMMapper
11
12 -in ${param_in}
13 -tr ${param_tr}
14 -out ${param_out}
15 -precursor_tolerance ${param_precursor_tolerance}
16 -product_tolerance ${param_product_tolerance}
17 ${param_no-strict}
18 -threads \${GALAXY_SLOTS:-24}
19 </command>
20 <inputs>
21 <param name="param_in" type="data" format="mzML" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in)"/>
22 <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
23 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance)"/>
24 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance)"/>
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)"/>
26 </inputs>
27 <outputs>
28 <data name="param_out" label="Output file containing mapped chromatograms" format="mzML"/>
29 </outputs>
30 <help>**What it does**
31
32 MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
33
34
35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html
36
37 @REFERENCES@
38 </help>
39 </tool>