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1 <tool id="Protein_report_processig" name="SAINT pre-processing Peptideshaker Report">
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2 <description></description>
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3 <command interpreter="python">Protein_report_processing.py $input $Bait_file $use_metric $fasta_db $preybool
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4 "
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5 #for $ba in $bait
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6 ${ba.bait1}
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7 ${ba.assign}
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8 ${ba.T_C}
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9 #end for
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10 "
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11 \$INSTALL_RUN_PATH/ $bait_bool $bait_file_in $Inter_file $Prey_file
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12 </command>
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13 <requirements>
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14 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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15 </requirements>
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16 <inputs>
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17 <param format="dat" name="input" type="data" label="Scaffold or MaxQuant peptides Output" muliple="true"/>
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18 <param type="use_metric" name="type" label="Select Report File Value for Qunatification">
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19 <option value="#Validated Peptides">#Validated Peptides</option>
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20 <option value="#Peptides">#Peptides</option>
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21 <option value="#Unique">#Unique</option>
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22 <option value="#Validated PSMs">#Validated PSMs</option>
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23 <option value="#PSMs">#PSMs</option>
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24 </param>
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25 <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
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26 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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27 <param name="bait_bool" type="boolean" checked="true" label="Are You Providing Your Own bait file?"/>
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28 <param type="data" format="dat" name="bait_file_in" label="Bait File" optional="true"/>
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29 <repeat name="bait" title="Bait Create">
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30 <param name="bait1" type="text" size="100" label="Bait"/>
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31 <param name="assign" type="text" size="100" label="Group Assignment"/>
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32 <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
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33 </repeat>
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34
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35 </inputs>
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36 <outputs>
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37 <data format="txt" name="Inter_file" label="Inter File"/>
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38 <data format="txt" name="Prey_file" label="Prey File" />
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39 <data format="txt" name="Bait_file" label="Bait File" />
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40 </outputs>
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41 <stdio>
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42 <regex match="Error: bad bait"
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43 source="stdout"
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44 level="fatal"
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45 description="Error: bad bait"/>
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46 <regex match="IOError: [Errno 2] No such file or directory: './tukeys_output.txt'"
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47 source="stderr"
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48 level="fatal"
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49 description="Error: Scaffold/MaxQuant mismatch. Check job settings."/>
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50 <regex match="bait_temp_file = open(sys.argv[10], 'r')"
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51 source="stderr"
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52 level="fatal"
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53 description="Error: Bait create settings mismatch. Check job settings."/>
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54 <regex match="Error|error"
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55 source="stdout"
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56 level="fatal"
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57 description="Unknown error"/>
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58 <regex match="Error|error"
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59 source="stderr"
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60 level="fatal"
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61 description="Unknown error"/>
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62 </stdio>
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63
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64 <tests>
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65 <test>
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66 <param name="input" value="fa_gc_content_input.fa"/>
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67 <output name="out_file1" file="fa_gc_content_output.txt"/>
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68 </test>
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69 </tests>
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70 <help>
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71 </help>
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72 </tool>
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