Mercurial > repos > galaxyp > openms_mrmmapper

annotate MRMMapper.xml @ 13:e6a97fe4a41f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:06:35 -0400
parents d7bae0606b34
children 63f4e28bcf1a
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="MRMMapper" name="MRMMapper" version="2.3.0">
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5 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MRMMapper</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command detect_errors="aggressive"><![CDATA[MRMMapper
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_tr:
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19 -tr $param_tr
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_precursor_tolerance:
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25 -precursor_tolerance $param_precursor_tolerance
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26 #end if
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27 #if $param_product_tolerance:
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28 -product_tolerance $param_product_tolerance
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29 #end if
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30 #if $param_no_strict:
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31 -no-strict
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32 #end if
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33 #if $param_allow_multiple_mappings:
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34 -allow_multiple_mappings
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35 #end if
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36 #if $adv_opts.adv_opts_selector=='advanced':
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37 #if $adv_opts.param_force:
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38 -force
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39 #end if
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40 #end if
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41 ]]></command>
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42 <inputs>
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43 <param name="param_in" type="data" format="mzml" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in) "/>
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44 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
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45 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance) "/>
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46 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance) "/>
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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) "/>
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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) "/>
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49 <expand macro="advanced_options">
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50 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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51 </expand>
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52 </inputs>
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53 <outputs>
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54 <data name="param_out" format="mzml"/>
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55 </outputs>
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56 <help>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
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57
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58
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59 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MRMMapper.html</help>
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60 </tool>