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1 <tool id="omssa_adapter" version="0.1.0" name="OMSSA (OpenMS)">
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2 <description>
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3 </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="stdio" />
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8 <expand macro="requires">
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9 <requirement type="package">omssa</requirement>
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10 <requirement type="package">blast+</requirement>
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2
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11 </expand>
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12 <command interpreter="python">
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13 openms_wrapper.py
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14 --executable '__SHELL__' --config $setup
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15 --executable 'OMSSAAdapter' --config $config
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16 </command>
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17 <configfiles>
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18 <configfile name="setup">
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19 ln -s $database db.fasta; makeblastdb -dbtype prot -parse_seqids -in 'db.fasta'
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20 </configfile>
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21 <configfile name="config">[simple_options]
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22 in=$input1
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23 out=$out
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24 database=db.fasta.psq
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25 omssa_executable=@WHICH(omssacl)@
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26 variable_modifications=${variable_modifications or ''}
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27 fixed_modifications=${fixed_modifications or ''}
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28 precursor_mass_tolerance=$precursor_mass_tolerance
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29 #if $precursor_mass_tolerance_unit == "ppm"
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30 precursor_mass_tolerance_unit_ppm=true
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31 #end if
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32 fragment_mass_tolerance=$fragment_mass_tolerance
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33 min_precursor_charge=$min_precursor_charge
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34 max_precursor_charge=$max_precursor_charge
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35 v=$v
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36 e=$e
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37 hl=$hl
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38 he=$he
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39 threads=4
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40 </configfile>
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41 </configfiles>
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42 <inputs>
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43 <expand macro="id_inputs" />
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44 <expand macro="fixed_modifications_param" />
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45 <expand macro="variable_modifications_param" />
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46 <expand macro="precursor_mass_tolerance_param" />
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47 <expand macro="precursor_mass_tolerance_unit_param" />
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48 <expand macro="fragment_mass_tolerance_param" />
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49 <expand macro="precursor_charge_params" />
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50 <param name="v" label="Maximum Number of Missed Cleavages" value="1" type="integer" />
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51 <param name="e" label="Enzyme" type="select">
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52 <option value="0" selected="true">Trypsin</option>
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53 <option value="1">Arg-C</option>
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54 <option value="2">CNBr</option>
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55 <option value="3">Chymotrypsin (FYWL)</option>
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56 <option value="4">Formic Acid</option>
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57 <option value="5">Lys-C</option>
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58 <option value="6">Lys-C, no P rule</option>
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59 <option value="7">Pepsin A</option>
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60 <option value="8">Trypsin+CNBr</option>
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61 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
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62 <option value="10">Trypsin, no P rule</option>
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63 <option value="11">Whole protein</option>
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64 <option value="12">Asp-N</option>
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65 <option value="13">Glu-C</option>
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66 <option value="14">Asp-N+Glu-C</option>
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67 <option value="15">Top-Down</option>
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68 <option value="16">Semi-Tryptic</option>
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69 <option value="17">No Enzyme</option>
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70 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
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71 <option value="19">Asp-N (DE)</option>
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72 <option value="20">Glu-C (DE)</option>
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73 <option value="21">Lys-N (K)</option>
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74 <option value="22">Thermolysin, no P rule</option>
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75 <option value="23">Semi-Chymotrypsin (FYWL)</option>
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76 <option value="24">Semi-Glu-C</option>
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77 </param>
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78 <param name="hl" label="Maximum Hits Per Spectrum" type="integer" value="30" />
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79 <param name="he" label="Maximum Hits Per Spectrum" type="float" value="1000" help="The maximum e-value allowed in the hit list. If you set this parameter too small (e.g., he=1), this will effectively introduce FDR filtering. Thus, allowing a less stringent FDR during post-processing will nevertheless return the (better) FDR introduced here, since mediocre hits are not even reported. " />
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80 </inputs>
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81 <expand macro="id_outputs" />
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82 <help>
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83 **What it does**
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84
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85
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86 **Citation**
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87
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88 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 ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.
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89
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90 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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91 </help>
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92 </tool>
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