Mercurial > repos > galaxyp > openms_idrtcalibration

annotate IDRTCalibration.xml @ 5:5f414e1b5b9d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 17:58:45 -0500
parents 4c3732da1276
children 47540d47277e
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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: [ID Processing]-->
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4 <tool id="IDRTCalibration" name="IDRTCalibration" version="2.2.0">
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5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDRTCalibration</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>IDRTCalibration
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14
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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_out:
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19 -out $param_out
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20 #end if
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21 #if $param_calibrant_1_reference:
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22 -calibrant_1_reference $param_calibrant_1_reference
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23 #end if
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24 #if $param_calibrant_2_reference:
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25 -calibrant_2_reference $param_calibrant_2_reference
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26 #end if
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27 #if $param_calibrant_1_input:
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28 -calibrant_1_input $param_calibrant_1_input
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29 #end if
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30 #if $param_calibrant_2_input:
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31 -calibrant_2_input $param_calibrant_2_input
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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_in" type="data" format="idxml" optional="False" label="input file" help="(-in) "/>
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41 <param name="param_calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help="(-calibrant_1_reference) "/>
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42 <param name="param_calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help="(-calibrant_2_reference) "/>
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43 <param name="param_calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
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44 <param name="param_calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed"/>
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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="idxml"/>
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51 </outputs>
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52 <help>Can be used to calibrate RTs of peptide hits linearly to standards.
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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/TOPP_IDRTCalibration.html</help>
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56 </tool>