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1 <tool id="xtandem_adapter" version="0.1.0" name="X! Tandem (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">tandem</requirement>
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10 </expand>
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11 <command interpreter="python">
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12 openms_wrapper.py
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13 --executable 'XTandemAdapter' --config $config
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14 </command>
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15 <configfiles>
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16 <configfile name="config">[simple_options]
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17 in=$input1
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18 out=$out
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19 database=$database
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20 xtandem_executable=@WHICH(tandem)@
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21 variable_modifications=${variable_modifications or ''}
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22 fixed_modifications=${fixed_modifications or ''}
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23 precursor_mass_tolerance=$precursor_mass_tolerance
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24 precursor_error_units=$precursor_mass_tolerance_unit
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25 fragment_mass_tolerance=$fragment_mass_tolerance
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26 fragment_error_units=$fragment_mass_tolerance_unit
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27 min_precursor_charge=$min_precursor_charge
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28 max_precursor_charge=$max_precursor_charge
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29 cleavage_site=$cleavage_site
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30 minimum_fragment_mz=$minimum_fragment_mz
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31 max_valid_expect=$max_valid_expect
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32 refinement=$refinement
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33 semi_cleavage=$semi_cleavage
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34 </configfile>
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35 </configfiles>
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36 <inputs>
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37 <expand macro="id_inputs" />
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38 <expand macro="fixed_modifications_param" />
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39 <expand macro="variable_modifications_param" />
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40 <expand macro="precursor_mass_tolerance_param" />
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41 <expand macro="precursor_mass_tolerance_unit_param" />
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42 <expand macro="fragment_mass_tolerance_param" />
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43 <expand macro="fragment_mass_tolerance_unit_param" />
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44 <expand macro="precursor_charge_params" />
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45 <param name="cleavage_site" label="Cleavage Site" type="select">
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46 <option value="[R]|{P}">argc</option>
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47 <option value="[X]|[D]">aspn</option>
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48 <option value="[FMWY]|{P}">chymotrypsin</option>
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49 <option value="[R]|[X]">clostripain</option>
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50 <option value="[M]|{P}">cnbr</option>
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51 <option value="[AGILV]|{P}">elastase</option>
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52 <option value="[D]|{P}">formicacid</option>
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53 <option value="[DE]|{P}">gluc</option>
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54 <option value="[E]|{P}">gluc_bicarb</option>
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55 <option value="[W]|[X]">iodosobenzoate</option>
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56 <option value="[K]|[P]">lysc</option>
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57 <option value="[K]|[X]">lysc-p</option>
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58 <option value="[X]|[K]">lysn</option>
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59 <option value="[X]|[AKRS]">lysn_promisc</option>
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60 <option value="[X]|[X]">nonspecific</option>
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61 <option value="[FL]|[X]">pepsina</option>
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62 <option value="[P]|[X]">protein_endopeptidase</option>
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63 <option value="[E]|[X]">staph_protease</option>
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64 <option value="[KR]|{P}" selected="true">trypsin</option>
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65 <option value="[DEKR]|{P}">trypsin_gluc</option>
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66 <option value="[K]|{P}">trypsin_k</option>
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67 <option value="[R]|{P}">trypsin_r</option>
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68 <sanitizer>
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69 <valid>
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70 <add value="{"/>
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71 <add value="}"/>
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72 <add value="|"/>
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73 <add value="["/>
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74 <add value="]"/>
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75 </valid>
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76 </sanitizer>
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77 </param>
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78 <param name="minimum_fragment_mz" label="Minimum Fragment m/z" value="150" type="float" />
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79 <param name="max_valid_expect" label="Maximum Valid E-Value to be Reported" value=".1" type="float" />
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80 <param name="semi_cleavage" type="boolean" label="Enable Semi-Cleavage" checked="false" truevalue="true" falsevalue="false" help="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." />
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81 <param name="refinement" type="boolean" label="Enable Refinement" checked="false" truevalue="true" falsevalue="false" help="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." />
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82 </inputs>
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83 <expand macro="id_outputs" />
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84 <help>
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85 **What it does**
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86
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87
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88 **Citation**
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89
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90 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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91
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92 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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93 </help>
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94 </tool>
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