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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="DecoyDatabase" name="DecoyDatabase" version="2.0.0">
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3 <description>Create decoy peptide databases from normal ones.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">DecoyDatabase</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>DecoyDatabase
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 #if $param_out:
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17 -out $param_out
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18 #end if
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19 #if $param_decoy_string:
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20 -decoy_string "$param_decoy_string"
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21 #end if
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22 #if $param_decoy_string_position:
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23 -decoy_string_position
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24 #if " " in str($param_decoy_string_position):
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25 "$param_decoy_string_position"
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26 #else
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27 $param_decoy_string_position
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28 #end if
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29 #end if
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30 #if $param_append:
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31 -append
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32 #end if
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33 #if $param_shuffle:
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34 -shuffle
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35 #end if
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36 -threads \${GALAXY_SLOTS:-24}
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37 #if $adv_opts.adv_opts_selector=='advanced':
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38 #if $adv_opts.param_force:
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39 -force
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40 #end if
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41 #end if
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42 </command>
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43 <inputs>
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44 <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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45 <sanitizer>
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46 <valid initial="string.printable">
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47 <remove value="'"/>
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48 <remove value="""/>
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49 </valid>
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50 </sanitizer>
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51 </param>
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52 <param name="param_decoy_string" type="text" size="30" value="_rev" label="String that is appended to the accession of the protein database to indicate a decoy protein" help="(-decoy_string) ">
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53 <sanitizer>
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54 <valid initial="string.printable">
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55 <remove value="'"/>
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56 <remove value="""/>
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57 </valid>
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58 </sanitizer>
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59 </param>
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60 <param name="param_decoy_string_position" type="select" optional="True" value="suffix" label="Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?" help="(-decoy_string_position) ">
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61 <option value="prefix">prefix</option>
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62 <option value="suffix">suffix</option>
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63 </param>
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64 <param name="param_append" type="boolean" truevalue="-append" falsevalue="" checked="false" optional="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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65 <param name="param_shuffle" type="boolean" truevalue="-shuffle" falsevalue="" checked="false" optional="True" label="If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed" help="(-shuffle) "/>
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66 <expand macro="advanced_options">
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67 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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68 </expand>
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69 </inputs>
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70 <outputs>
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71 <data name="param_out" format="fasta"/>
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72 </outputs>
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73 <help>**What it does**
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74
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75 Create decoy peptide databases from normal ones.
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76
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77
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78 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DecoyDatabase.html</help>
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79 <expand macro="references"/>
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80 </tool>
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