Mercurial > repos > galaxyp > openms_rnpxlxicfilter

annotate RNPxlXICFilter.xml @ 0:4de461b0c05d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:33:47 -0500
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4de461b0c05d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="2.1.0">
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5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">RNPxlXICFilter</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>RNPxlXICFilter
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14
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15 #if $param_control:
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16 -control $param_control
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17 #end if
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18 #if $param_treatment:
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19 -treatment $param_treatment
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20 #end if
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21 #if $param_fold_change:
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22 -fold_change $param_fold_change
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23 #end if
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24 #if $param_rt_tol:
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25 -rt_tol $param_rt_tol
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26 #end if
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27 #if $param_mz_tol:
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28 -mz_tol $param_mz_tol
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29 #end if
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30 #if $param_out:
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31 -out $param_out
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32 #end if
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33 #if $adv_opts.adv_opts_selector=='advanced':
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34 #if $adv_opts.param_force:
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35 -force
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36 #end if
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37 #end if
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38 </command>
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39 <inputs>
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40 <param name="param_control" type="data" format="mzml" optional="False" label="input mzML file" help="(-control) "/>
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41 <param name="param_treatment" type="data" format="mzml" optional="False" label="input mzML file" help="(-treatment) "/>
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42 <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change) "/>
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43 <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
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44 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
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45 <expand macro="advanced_options">
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46 <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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47 </expand>
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48 </inputs>
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49 <outputs>
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50 <data name="param_out" format="mzml"/>
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51 </outputs>
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52 <help>Remove MS2 spectra from treatment based on the fold change between control and treatment.
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxlXICFilter.html</help>
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56 </tool>