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annotate DecoyDatabase.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -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: [Utilities]-->
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4 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.0.0">
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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 $param_decoy_string:
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23 -decoy_string &quot;$param_decoy_string&quot;
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24 #end if
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25 #if $param_decoy_string_position:
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26 -decoy_string_position
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27 #if &quot; &quot; in str($param_decoy_string_position):
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28 &quot;$param_decoy_string_position&quot;
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29 #else
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30 $param_decoy_string_position
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31 #end if
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32 #end if
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33 #if $param_append:
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34 -append
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35 #end if
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36 #if $param_shuffle:
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37 -shuffle
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38 #end if
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39 -threads \${GALAXY_SLOTS:-24}
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40 #if $adv_opts.adv_opts_selector=='advanced':
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #end if
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45 </command>
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46 <inputs>
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47 <param format="fasta" help="(-in) It is recommended to include a contaminant database as well" label="Input FASTA file(s), each containing a database" multiple="true" name="param_in" optional="False" size="30" type="data">
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48 <sanitizer>
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49 <valid initial="string.printable">
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50 <remove value="'"/>
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51 <remove value="&quot;"/>
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52 </valid>
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53 </sanitizer>
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54 </param>
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55 <param help="(-decoy_string) " label="String that is appended to the accession of the protein database to indicate a decoy protein" name="param_decoy_string" size="30" type="text" value="_rev">
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56 <sanitizer>
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57 <valid initial="string.printable">
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58 <remove value="'"/>
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59 <remove value="&quot;"/>
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60 </valid>
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61 </sanitizer>
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62 </param>
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63 <param help="(-decoy_string_position) " label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" name="param_decoy_string_position" optional="True" type="select" value="suffix">
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64 <option value="prefix">prefix</option>
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65 <option value="suffix">suffix</option>
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66 </param>
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67 <param checked="false" falsevalue="" help="(-append) " label="If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches" name="param_append" optional="True" truevalue="-append" type="boolean"/>
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68 <param checked="false" falsevalue="" help="(-shuffle) " label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" name="param_shuffle" optional="True" truevalue="-shuffle" type="boolean"/>
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69 <expand macro="advanced_options">
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70 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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71 </expand>
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72 </inputs>
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73 <outputs>
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74 <data format="fasta" name="param_out"/>
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75 </outputs>
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76 <help>Create decoy peptide databases from normal ones.
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77
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78
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79 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
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80 </tool>