Mercurial > repos > galaxyp > openms_phosphoscoring

annotate PhosphoScoring.xml @ 0:0a1e6a367122 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 12:33:19 -0500
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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="PhosphoScoring" name="PhosphoScoring" version="2.1.0">
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5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PhosphoScoring</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>PhosphoScoring
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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_id:
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19 -id $param_id
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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_fragment_mass_tolerance:
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25 -fragment_mass_tolerance $param_fragment_mass_tolerance
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26 #end if
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27 #if $param_fragment_mass_unit:
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28 -fragment_mass_unit $param_fragment_mass_unit
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29 #end if
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30 #if $param_max_peptide_length:
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31 -max_peptide_length $param_max_peptide_length
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32 #end if
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33 #if $param_max_num_perm:
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34 -max_num_perm $param_max_num_perm
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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 with MS/MS spectra" help="(-in) "/>
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44 <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/>
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45 <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/>
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46 <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) ">
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47 <option value="Da" selected="true">Da</option>
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48 <option value="ppm">ppm</option>
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49 </param>
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50 <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/>
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51 <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/>
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52 <expand macro="advanced_options">
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53 <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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54 </expand>
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55 </inputs>
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56 <outputs>
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57 <data name="param_out" format="idxml"/>
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58 </outputs>
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59 <help>Scores potential phosphorylation sites in order to localize the most probable sites.
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60
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61
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62 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PhosphoScoring.html</help>
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63 </tool>