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1 <tool id="compnovo" version="0.1.0" name="CompNovo (OpenMS)">
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2 <description>
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3 Performs a de novo peptide identification using the CompNovo engine.
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4 </description>
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5 <macros>
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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="requires" />
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10 <command interpreter="python">
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11 #if str($mode) == "cid"
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12 #set $executable = "CompNovoCID"
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13 #else
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14 #set $executable = "CompNovo"
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15 #end if
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16 openms_wrapper.py --executable '$executable' --config $config
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17 </command>
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18 <configfiles>
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19 <configfile name="config">[simple_options]
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20 in=${input1}
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21 out=${out}
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22 #set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
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23 #if $fixed_mods_str
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24 algorithm!fixed_modifications=$fixed_mods_str
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25 #end if
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26 #set $variable_mods_str=",".join([str($variable_mod.fixed_mod) for $variable_mod in $variable_mods])
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27 #if $variable_mods_str
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28 algorithm!variable_modifications=$variable_mods_str
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29 #end if
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30 </configfile>
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31 </configfiles>
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32 <inputs>
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33 <param name="input1" type="data" format="mzml" label="Input peak list" />
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34 <param name="mode" type="select" label="Mode">
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35 <option value="cid">CID-only</option>
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36 <option value="cidetd">CID/ETD</option>
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37 </param>
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38 <repeat name="fixed_mods" title="Fixed Modification">
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39 <param name="fixed_mod" type="select" label="Fixed Modification">
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40 <options from_file="openms_mods.loc">
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41 <column name="name" index="0" />
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42 <column name="value" index="0" />
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43 </options>
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44 </param>
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45 </repeat>
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46 <repeat name="variable_mods" title="Variable Modification">
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47 <param name="variable_mod" type="select" label="Variable Modification">
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48 <options from_file="openms_mods.loc">
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49 <column name="name" index="0"/>
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50 <column name="value" index="0" />
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51 </options>
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52 </param>
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53 </repeat>
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54 </inputs>
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55 <outputs>
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56 <data format="idxml" name="out" />
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57 </outputs>
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58 <help>
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59 **What it does**
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60
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61 De novo peptide sequencing of mass spectrometry data.
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62
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63 **Citation**
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64
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65 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, et al.: De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 2009, 30:3736-3747.``
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66
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67 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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68 </help>
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69 </tool>
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