Mercurial > repos > galaxyp > openms_decoydatabase

annotate DecoyDatabase.xml @ 0:bb36816527e8 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 09:55:50 -0500
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bb36816527e8 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="DecoyDatabase" name="DecoyDatabase" version="2.1.0">
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5 <description>Create decoy peptide databases from normal ones.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">DecoyDatabase</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>DecoyDatabase
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_decoy_string:
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23 -decoy_string "$param_decoy_string"
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24 #end if
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25 #if $param_decoy_string_position:
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26 -decoy_string_position $param_decoy_string_position
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27 #end if
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28 #if $param_append:
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29 -append $param_append
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30 #end if
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31 #if $param_method:
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32 -method $param_method
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33 #end if
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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 name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input FASTA file(s), each containing a database" help="(-in) It is recommended to include a contaminant database as well">
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42 <sanitizer>
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43 <valid initial="string.printable">
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44 <remove value="'"/>
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45 <remove value="&quot;"/>
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46 </valid>
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47 </sanitizer>
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48 </param>
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49 <param name="param_decoy_string" type="text" size="30" value="DECOY_" label="String that is combined with the accession of the protein identifier to indicate a decoy protein" help="(-decoy_string) ">
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50 <sanitizer>
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51 <valid initial="string.printable">
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52 <remove value="'"/>
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53 <remove value="&quot;"/>
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54 </valid>
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55 </sanitizer>
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56 </param>
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57 <param name="param_decoy_string_position" display="radio" type="select" optional="False" value="prefix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
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58 <option value="prefix" selected="true">prefix</option>
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59 <option value="suffix">suffix</option>
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60 </param>
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61 <param name="param_append" display="radio" type="select" optional="False" value="true" label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" help="(-append) ">
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62 <option value="true" selected="true">true</option>
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63 <option value="false">false</option>
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64 </param>
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65 <param name="param_method" display="radio" type="select" optional="False" value="reverse" label="Method by which decoy sequences are generated from target sequences" help="(-method) ">
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66 <option value="reverse" selected="true">reverse</option>
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67 <option value="shuffle">shuffle</option>
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68 </param>
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69 <expand macro="advanced_options">
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70 <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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71 </expand>
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72 </inputs>
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73 <outputs>
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74 <data name="param_out" format="fasta"/>
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75 </outputs>
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76
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77 <tests>
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78 <test>
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79 <param name="param_in" value="DecoyDatabase_input.fasta"/>
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80 <output name="param_out" file="DecoyDatabase_output.fasta"/>
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81 </test>
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82 </tests>
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83
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84 <help>Create decoy peptide databases from normal ones.
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85
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86
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87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
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88 </tool>