annotate XFDR.xml @ 0:b19847e8f0a1 draft

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author galaxyp
date Mon, 12 Feb 2018 13:27:44 -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 CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="XFDR" name="XFDR" version="2.3.0">
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5 <description>Calculates false discovery rate estimates on crosslink identifications</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">XFDR</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>XFDR
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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_idXML:
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19 -out_idXML $param_out_idXML
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20 #end if
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21 #if $param_out_mzIdentML:
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22 -out_mzIdentML $param_out_mzIdentML
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23 #end if
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24 #if $param_minborder:
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25 -minborder $param_minborder
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26 #end if
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27 #if $param_maxborder:
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28 -maxborder $param_maxborder
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29 #end if
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30 #if $param_mindeltas:
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31 -mindeltas $param_mindeltas
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32 #end if
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33 #if $param_minionsmatched:
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34 -minionsmatched $param_minionsmatched
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35 #end if
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36 #if $param_uniquexl:
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37 -uniquexl
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38 #end if
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39 #if $param_no_qvalues:
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40 -no_qvalues
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41 #end if
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42 #if $param_minscore:
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43 -minscore $param_minscore
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44 #end if
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45 #if $adv_opts.adv_opts_selector=='advanced':
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #end if
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50 </command>
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51 <inputs>
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52 <param name="param_in" type="data" format="xml,idxml,mzid" optional="True" label="Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)" help="(-in) "/>
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53 <param name="param_minborder" type="integer" value="-1" label="Filter for minimum precursor mass error (ppm)" help="(-minborder) Can only be applied for xquest.xml input"/>
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54 <param name="param_maxborder" type="integer" value="-1" label="Filter for maximum precursor mass error (ppm)" help="(-maxborder) Can only be applied for xquest.xml input"/>
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55 <param name="param_mindeltas" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Filter for delta score, 0 is no filte" help="(-mindeltas) Minimum delta score required, hits are rejected if larger or equal. Can only be applied for xquest.xml input"/>
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56 <param name="param_minionsmatched" type="integer" min="0" optional="True" value="0" label="Filter for minimum matched ions per peptide" help="(-minionsmatched) Can only be applied for xquest.xml input"/>
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57 <param name="param_uniquexl" display="radio" type="boolean" truevalue="-uniquexl" falsevalue="" checked="false" optional="True" label="Calculate statistics based on unique IDs" help="(-uniquexl) Can only be applied for xquest.xml input"/>
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58 <param name="param_no_qvalues" display="radio" type="boolean" truevalue="-no_qvalues" falsevalue="" checked="false" optional="True" label="Do not transform simple FDR to q-values" help="(-no_qvalues) "/>
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59 <param name="param_minscore" type="integer" value="0" label="Minimum score to be considered for FDR calculation" help="(-minscore) "/>
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60 <expand macro="advanced_options">
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61 <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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62 </expand>
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63 </inputs>
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64 <outputs>
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65 <data name="param_out_idXML" format="idxml"/>
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66 <data name="param_out_mzIdentML" format="mzid"/>
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67 </outputs>
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68 <help>Calculates false discovery rate estimates on crosslink identifications
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69
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70
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71 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_XFDR.html</help>
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72 </tool>