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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PILISIdentification" name="PILISIdentification" version="1.12.0">
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3 <description>performs a peptide/protein identification with the PILIS engine</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">PILISIdentification</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>PILISIdentification
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -model_file ${param_model_file}
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15 -peptide_db_file ${param_peptide_db_file}
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16 -precursor_mass_tolerance ${param_precursor_mass_tolerance}
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17 -peak_mass_tolerance ${param_peak_mass_tolerance}
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18 -max_pre_candidates ${param_max_pre_candidates}
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19 -max_candidates ${param_max_candidates}
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20 -upper_mz ${param_upper_mz}
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21 -lower_mz ${param_lower_mz}
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22 -fixed_modifications ${param_fixed_modifications}
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23 -threads \${GALAXY_SLOTS:-24}
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24 -model:charge_directed_threshold ${param_charge_directed_threshold}
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25 -model:charge_remote_threshold ${param_charge_remote_threshold}
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26 -model:charge_loss_factor ${param_charge_loss_factor}
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27 -model:min_y_ion_intensity ${param_min_y_ion_intensity}
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28 -model:min_b_ion_intensity ${param_min_b_ion_intensity}
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29 -model:min_a_ion_intensity ${param_min_a_ion_intensity}
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30 -model:min_y_loss_intensity ${param_min_y_loss_intensity}
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31 -model:min_b_loss_intensity ${param_min_b_loss_intensity}
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32 -model:visible_model_depth ${param_visible_model_depth}
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33 -model:model_depth ${param_model_depth}
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34 ${param_use_local_scoring}
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35 ${param_do_not_use_evalue_scoring}
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36 -scoring:survival_function_bin_size ${param_survival_function_bin_size}
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37 -scoring:global_linear_fitting_threshold ${param_global_linear_fitting_threshold}
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38 -scoring:local_linear_fitting_threshold ${param_local_linear_fitting_threshold}
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39 </command>
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40 <inputs>
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41 <param name="param_in" type="data" format="mzML" optional="False" label="input file in MzML format" help="(-in)"/>
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42 <param name="param_model_file" type="data" format="data" label="the model file of the PILISModel" help="(-model_file)"/>
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43 <param name="param_peptide_db_file" type="data" format="data" label="a file which should contain peptides in the format#br#DFPIANGER 1019.09 1#br#where the first column is the peptide, the second the m/z#br#the third the charge. As a alternative the sequence file#br#may contain only peptide sequences each in a separate line#br#repectively" help="(-peptide_db_file)"/>
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44 <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance)"/>
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45 <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance)"/>
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46 <param name="param_max_pre_candidates" type="integer" value="200" label="number of candidates that are used for precise scoring" help="(-max_pre_candidates)"/>
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47 <param name="param_max_candidates" type="integer" value="20" label="number of candidates that are reported by PILIS" help="(-max_candidates)"/>
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48 <param name="param_upper_mz" type="float" value="2000.0" label="upper mz interval endpoint" help="(-upper_mz)"/>
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49 <param name="param_lower_mz" type="float" value="200.0" label="lower mz interval endpoint" help="(-lower_mz)"/>
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50 <param name="param_fixed_modifications" type="text" size="20" label="monoisotopic_mass@residues e.g.: 57.021464@C" help="(-fixed_modifications)"/>
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51 <param name="param_charge_directed_threshold" type="float" value="0.3" label="bla" help="(-charge_directed_threshold)"/>
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52 <param name="param_charge_remote_threshold" type="float" value="0.2" label="bla" help="(-charge_remote_threshold)"/>
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53 <param name="param_charge_loss_factor" type="float" value="0.5" label="bla" help="(-charge_loss_factor)"/>
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54 <param name="param_min_y_ion_intensity" type="float" value="0.2" label="" help="(-min_y_ion_intensity)"/>
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55 <param name="param_min_b_ion_intensity" type="float" value="0.15" label="" help="(-min_b_ion_intensity)"/>
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56 <param name="param_min_a_ion_intensity" type="float" value="0.05" label="" help="(-min_a_ion_intensity)"/>
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57 <param name="param_min_y_loss_intensity" type="float" value="0.05" label="" help="(-min_y_loss_intensity)"/>
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58 <param name="param_min_b_loss_intensity" type="float" value="0.02" label="" help="(-min_b_loss_intensity)"/>
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59 <param name="param_visible_model_depth" type="integer" value="30" label="bla" help="(-visible_model_depth)"/>
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60 <param name="param_model_depth" type="integer" value="4" label="bla" help="(-model_depth)"/>
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61 <param name="param_use_local_scoring" type="boolean" truevalue="-scoring:use_local_scoring true" falsevalue="-scoring:use_local_scoring false" checked="false" optional="True" label="..." help="(-use_local_scoring)"/>
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62 <param name="param_do_not_use_evalue_scoring" type="boolean" truevalue="-scoring:do_not_use_evalue_scoring true" falsevalue="-scoring:do_not_use_evalue_scoring false" checked="false" optional="True" label="..." help="(-do_not_use_evalue_scoring)"/>
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63 <param name="param_survival_function_bin_size" type="integer" value="20" label="..." help="(-survival_function_bin_size)"/>
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64 <param name="param_global_linear_fitting_threshold" type="float" value="0.1" label="..." help="(-global_linear_fitting_threshold)"/>
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65 <param name="param_local_linear_fitting_threshold" type="float" value="0.5" label="..." help="(-local_linear_fitting_threshold)"/>
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66 </inputs>
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67 <outputs>
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68 <data name="param_out" label="output file in idXML format" format="idXML"/>
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69 </outputs>
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70 <help>**What it does**
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71
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72 performs a peptide/protein identification with the PILIS engine
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73
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74
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PILISIdentification.html
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76
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77 @REFERENCES@
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78 </help>
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79 </tool>
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