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annotate IDRTCalibration.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
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6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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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="2.0.0">
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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 -threads \${GALAXY_SLOTS:-24}
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34 #if $adv_opts.adv_opts_selector=='advanced':
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35 #if $adv_opts.param_force:
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36 -force
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37 #end if
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38 #end if
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39 </command>
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40 <inputs>
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41 <param format="xml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
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42 <param help="(-calibrant_1_reference) " label="The RT of the first calibrant in the reference file" name="param_calibrant_1_reference" type="float" value="0.1"/>
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43 <param help="(-calibrant_2_reference) " label="The RT of the second calibrant in the reference file" name="param_calibrant_2_reference" type="float" value="0.9"/>
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44 <param help="(-calibrant_1_input) Please note that this value needs to be set. The default value -1.0 is not allowed" label="The RT of the first calibrant in the input file" name="param_calibrant_1_input" type="float" value="-1.0"/>
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45 <param help="(-calibrant_2_input) Please note that this value needs to be set. The default value -1.0 is not allowed" label="The RT of the second calibrant in the input file" name="param_calibrant_2_input" type="float" value="-1.0"/>
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46 <expand macro="advanced_options">
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47 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data format="xml" name="param_out"/>
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52 </outputs>
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53 <help>Can be used to calibrate RTs of peptide hits linearly to standards.
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54
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55
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56 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDRTCalibration.html</help>
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57 </tool>