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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDMerger" name="IDMerger" version="2.0.0">
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3 <description>Merges several protein/peptide identification files into one file.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDMerger</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>IDMerger
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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_add_to:
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20 -add_to $param_add_to
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21 #end if
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22 #if $param_annotate_file_origin:
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23 -annotate_file_origin
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24 #end if
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25 #if $param_pepxml_protxml:
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26 -pepxml_protxml
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27 #end if
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28 -threads \${GALAXY_SLOTS:-24}
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29 #if $adv_opts.adv_opts_selector=='advanced':
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30 #if $adv_opts.param_force:
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31 -force
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32 #end if
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33 #end if
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34 </command>
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35 <inputs>
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36 <param name="param_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks" help="(-in) ">
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37 <sanitizer>
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38 <valid initial="string.printable">
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39 <remove value="'"/>
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40 <remove value="""/>
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 <param name="param_add_to" type="data" format="idxml" optional="True" label="Optional input file" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)"/>
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45 <param name="param_annotate_file_origin" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help="(-annotate_file_origin) "/>
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46 <param name="param_pepxml_protxml" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) <br>Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
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47 <expand macro="advanced_options">
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48 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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49 </expand>
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50 </inputs>
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51 <outputs>
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52 <data name="param_out" format="idxml"/>
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53 </outputs>
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54 <help>**What it does**
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55
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56 Merges several protein/peptide identification files into one file.
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57
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58
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59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help>
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60 <expand macro="references"/>
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61 </tool>
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