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annotate ident_params.xml @ 61:3ec27b4cee7c draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
author galaxyp
date Thu, 12 Aug 2021 14:06:52 +0000
parents 943a34df6047
children
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1 <tool id="ident_params"
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2 name="Identification Parameters"
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3 version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"
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4 profile="20.01"
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5 >
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6 <description>
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7 Sets the identification parameters to be used in SearchGUI and PeptideShaker apps
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8 </description>
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9 <macros>
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10 <import>macros_basic.xml</import>
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11 <import>macros_modifications.xml</import>
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12 </macros>
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13 <requirements>
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14 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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15 </requirements>
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16 <expand macro="stdio" />
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17 <command>
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18 <![CDATA[
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19 #set $bin_dir = "bin"
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21 mkdir output;
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22 cwd=`pwd`;
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23 export HOME=\$cwd;
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27 echo 'running Identification Parameters CLI' &&
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28 #####################################################
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29 ## generate IdentificationParameters for SearchGUI ##
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30 #####################################################
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31 searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
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32 --exec_dir="./bin/"
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33 -use_log_folder 0
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34 -out './IdentificationParametersOutput.par'
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35 ## SPECTRUM MATCHING PARAMETERS
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37 -frag_tol '${spectrum_matching_options.fragment_tol}'
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38 -frag_ppm '${spectrum_matching_options.fragment_tol_units}'
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39 -prec_tol '${spectrum_matching_options.precursor_ion_tol}'
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40 -prec_ppm '${spectrum_matching_options.precursor_ion_tol_units}'
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42 #if $spectrum_matching_options.digestion.cleavage == 'default':
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43 -mc $spectrum_matching_options.digestion.missed_cleavages
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44 #elif $spectrum_matching_options.digestion.cleavage == '0' and len($spectrum_matching_options.digestion.digests) > 0:
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45 #set $enzymes = []
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46 #set $missed_cleavages = []
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47 #set $specificities = []
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48 #for $i, $digest in enumerate($spectrum_matching_options.digestion.digests):
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49 #silent $enzymes.append(str($digest.enzyme))
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50 #silent $missed_cleavages.append(str($digest.missed_cleavages))
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51 #silent $specificities.append(str($digest.specificity))
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52 #end for
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53 -enzyme "#echo ','.join($enzymes)#"
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54 -mc "#echo ','.join($missed_cleavages)#"
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55 -specificity "#echo ','.join($specificities)#"
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56 #else:
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57 -digestion $spectrum_matching_options.digestion.cleavage
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58 #end if
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61 #set $fixed_mods_str = $spectrum_matching_options.fixed_modifications or ''
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62 #set $variable_mods_str = $spectrum_matching_options.variable_modifications or ''
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63 #if $fixed_mods_str
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64 -fixed_mods "$fixed_mods_str"
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65 #end if
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66 #if $variable_mods_str
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67 -variable_mods "$variable_mods_str"
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68 #end if
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71 -min_charge $spectrum_matching_options.min_charge
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72 -max_charge $spectrum_matching_options.max_charge
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73 -fi $spectrum_matching_options.forward_ion
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74 -ri $spectrum_matching_options.reverse_ion
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75 -min_isotope ${spectrum_matching_options.min_isotope}
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76 -max_isotope ${spectrum_matching_options.max_isotope}
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77 ## TODO: TO CHECK, these last two both are also present in the app in the import filters section.
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80 ## -- SEARCH ENGINES SPECIFIC PARAMETERS --
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82 ## XTANDEM ADVANCED SETTINGS
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84 #if $searchengines_options.xtandem.xtandem_advanced == "yes"
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85
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
86 ## Spectrum import
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
87 #if $searchengines_options.xtandem.xtandem_spectrum.xtandem_spectrum_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
88 -xtandem_dynamic_range ${searchengines_options.xtandem.xtandem_spectrum.xtandem_dynamic_range}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
89 -xtandem_npeaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_npeaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
90 -xtandem_min_frag_mz ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_frag_mz}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
91 -xtandem_min_peaks ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
92 -xtandem_noise_suppr ${searchengines_options.xtandem.xtandem_spectrum.xtandem_noise_suppr}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
93 -xtandem_min_prec_mass ${searchengines_options.xtandem.xtandem_spectrum.xtandem_min_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
94 -xtandem_parent_isotope_correction ${searchengines_options.xtandem.xtandem_spectrum.xtandem_parent_isotope_correction}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
95 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
96
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
97 ## Advanced search
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
98 #if $searchengines_options.xtandem.xtandem_asearch.xtandem_asearch_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
99 -xtandem_quick_acetyl ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_acetyl}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
100 -xtandem_quick_pyro ${searchengines_options.xtandem.xtandem_asearch.xtandem_quick_pyro}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
101 -xtandem_stp_bias ${searchengines_options.xtandem.xtandem_asearch.xtandem_stp_bias}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
102 -xtandem_ptm_complexity ${searchengines_options.xtandem.xtandem_asearch.xtandem_ptm_complexity}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
103 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
104
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
105 ## Output
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
106 #if $searchengines_options.xtandem.xtandem_output.xtandem_output_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
107 -xtandem_output_results $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
108 #if $searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_output_results_selector != "all"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
109 -xtandem_evalue ${searchengines_options.xtandem.xtandem_output.xtandem_output_results_conditional.xtandem_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
110 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
111 -xtandem_output_proteins ${searchengines_options.xtandem.xtandem_output.xtandem_output_proteins}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
112 -xtandem_output_sequences ${searchengines_options.xtandem.xtandem_output.xtandem_output_sequences}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
113 -xtandem_output_spectra ${searchengines_options.xtandem.xtandem_output.xtandem_output_spectra}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
114 -xtandem_output_histograms ${searchengines_options.xtandem.xtandem_output.xtandem_output_histograms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
115 ## TODO: Integration with Skyline not ready yet: -xtandem_skyline_path ${searchengines_options.xtandem.xtandem_output.xtandem_skyline_path}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
116 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
117
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
118 ## Refinement
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
119 #if $searchengines_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
120 -xtandem_refine 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
121 -xtandem_refine_evalue ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
122 -xtandem_refine_unc ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_unc}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
123 -xtandem_refine_semi ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_semi}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
124 -xtandem_refine_pot ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_pot}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
125 -xtandem_refine_p_mut ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
126 -xtandem_refine_snaps ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_snaps}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
127 -xtandem_refine_spec_synt ${searchengines_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
128 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
129 -xtandem_refine 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
130 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
131 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
132 -xtandem_output_spectra 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
133 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
134
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
135 ## MYRIMATCH ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
136
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
137 #if $searchengines_options.myrimatch.myrimatch_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
138 -myrimatch_min_pep_length ${searchengines_options.myrimatch.myrimatch_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
139 -myrimatch_max_pep_length ${searchengines_options.myrimatch.myrimatch_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
140 -myrimatch_min_prec_mass ${searchengines_options.myrimatch.myrimatch_min_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
141 -myrimatch_max_prec_mass ${searchengines_options.myrimatch.myrimatch_max_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
142 -myrimatch_num_matches ${searchengines_options.myrimatch.myrimatch_num_matches}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
143 -myrimatch_num_ptms ${searchengines_options.myrimatch.myrimatch_num_ptms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
144 -myrimatch_fragmentation ${searchengines_options.myrimatch.myrimatch_fragmentation}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
145 -myrimatch_termini ${searchengines_options.myrimatch.myrimatch_termini}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
146 -myrimatch_plus_three ${searchengines_options.myrimatch.myrimatch_plus_three}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
147 -myrimatch_xcorr ${searchengines_options.myrimatch.myrimatch_xcorr}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
148 -myrimatch_tic_cutoff ${searchengines_options.myrimatch.myrimatch_tic_cutoff}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
149 -myrimatch_intensity_classes ${searchengines_options.myrimatch.myrimatch_intensity_classes}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
150 -myrimatch_class_multiplier ${searchengines_options.myrimatch.myrimatch_class_multiplier}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
151 -myrimatch_num_batches ${searchengines_options.myrimatch.myrimatch_num_batches}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
152 -myrimatch_max_peak ${searchengines_options.myrimatch.myrimatch_max_peak}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
153 -myrimatch_output ${searchengines_options.myrimatch.myrimatch_output}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
154 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
155 -myrimatch_output mzIdentML
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
156 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
157
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
158
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
159 ## MSGF+ ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
160
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
161 #if $searchengines_options.msgf.msgf_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
162 -msgf_decoy ${searchengines_options.msgf.msgf_decoy}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
163 -msgf_instrument ${searchengines_options.msgf.msgf_instrument}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
164 -msgf_fragmentation ${searchengines_options.msgf.msgf_fragmentation}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
165 -msgf_protocol ${searchengines_options.msgf.msgf_protocol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
166 -msgf_termini ${searchengines_options.msgf.msgf_termini}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
167 -msgf_min_pep_length ${searchengines_options.msgf.msgf_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
168 -msgf_max_pep_length ${searchengines_options.msgf.msgf_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
169 -msgf_num_ptms ${searchengines_options.msgf.msgf_num_ptms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
170 -msgf_num_matches ${searchengines_options.msgf.msgf_num_matches}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
171 -msgf_additional ${searchengines_options.msgf.msgf_additional}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
172 #if $searchengines_options.msgf.msgf_tasks.msgf_tasks_custom == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
173 -msgf_num_tasks ${searchengines_options.msgf.msgf_tasks.msgf_num_tasks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
174 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
175 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
176
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
177
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
178 ## MSAMANDA ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
179
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
180 #if $searchengines_options.ms_amanda.ms_amanda_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
181 -ms_amanda_decoy ${searchengines_options.ms_amanda.ms_amanda_decoy}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
182 -ms_amanda_instrument "${searchengines_options.ms_amanda.ms_amanda_instrument}"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
183 -ms_amanda_max_rank ${searchengines_options.ms_amanda.ms_amanda_max_rank}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
184 -ms_amanda_mono ${searchengines_options.ms_amanda.ms_amanda_mono}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
185 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
186
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
187
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
188 ## ANDROMEDA ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
189
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
190 #* Not working in tests
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
191 #if $searchengines_options.andromeda.andromeda_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
192 -andromeda_max_pep_mass ${searchengines_options.andromeda.andromeda_max_pep_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
193 -andromeda_max_comb ${searchengines_options.andromeda.andromeda_max_comb}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
194 -andromeda_top_peaks ${searchengines_options.andromeda.andromeda_top_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
195 -andromeda_top_peaks_window ${searchengines_options.andromeda.andromeda_top_peaks_window}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
196 -andromeda_incl_water ${searchengines_options.andromeda.andromeda_incl_water}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
197 -andromeda_incl_ammonia ${searchengines_options.andromeda.andromeda_incl_ammonia}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
198 -andromeda_neutral_losses ${searchengines_options.andromeda.andromeda_neutral_losses}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
199 -andromeda_fragment_all ${searchengines_options.andromeda.andromeda_fragment_all}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
200 -andromeda_emp_correction ${searchengines_options.andromeda.andromeda_emp_correction}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
201 -andromeda_higher_charge ${searchengines_options.andromeda.andromeda_higher_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
202 -andromeda_equal_il ${searchengines_options.andromeda.andromeda_equal_il}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
203 -andromeda_frag_method ${searchengines_options.andromeda.andromeda_frag_method}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
204 -andromeda_max_mods ${searchengines_options.andromeda.andromeda_max_mods}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
205 -andromeda_min_pep_length ${searchengines_options.andromeda.andromeda_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
206 -andromeda_max_pep_length ${searchengines_options.andromeda.andromeda_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
207 -andromeda_max_psms ${searchengines_options.andromeda.andromeda_max_psms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
208 -andromeda_decoy_mode ${searchengines_options.andromeda.andromeda_decoy_mode}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
209 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
210 *#
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
211
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
212
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
213 ## OMSSA ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
214
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
215 #if $searchengines_options.omssa.omssa_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
216 ## Spectrum
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
217 #if $searchengines_options.omssa.omssa_spectrum.omssa_spectrum_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
218 -omssa_low_intensity "${searchengines_options.omssa.omssa_spectrum.omssa_low_intensity}"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
219 -omssa_high_intensity ${searchengines_options.omssa.omssa_spectrum.omssa_high_intensity}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
220 -omssa_intensity_incr ${searchengines_options.omssa.omssa_spectrum.omssa_intensity_incr}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
221 -omssa_min_peaks ${searchengines_options.omssa.omssa_spectrum.omssa_min_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
222 -omssa_remove_prec ${searchengines_options.omssa.omssa_spectrum.omssa_remove_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
223 -omssa_estimate_charge ${searchengines_options.omssa.omssa_spectrum.omssa_estimate_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
224 -omssa_plus_one ${searchengines_options.omssa.omssa_spectrum.omssa_plus_one}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
225 -omssa_fraction ${searchengines_options.omssa.omssa_spectrum.omssa_fraction}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
226 -omssa_prec_per_spectrum ${searchengines_options.omssa.omssa_spectrum.omssa_prec_per_spectrum}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
227 -omssa_scale_prec ${searchengines_options.omssa.omssa_spectrum.omssa_scale_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
228 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
229
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
230 ## Spectrum
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
231 #if $searchengines_options.omssa.omssa_database.omssa_database_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
232 -omssa_memory ${searchengines_options.omssa.omssa_database.omssa_memory}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
233 -omssa_methionine ${searchengines_options.omssa.omssa_database.omssa_methionine}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
234 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
235
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
236 ## Database
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
237 #if $searchengines_options.omssa.omssa_search.omssa_search_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
238 -omssa_neutron ${searchengines_options.omssa.omssa_search.omssa_neutron}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
239 -omssa_single_window_wd ${searchengines_options.omssa.omssa_search.omssa_single_window_wd}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
240 -omssa_double_window_wd ${searchengines_options.omssa.omssa_search.omssa_double_window_wd}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
241 -omssa_single_window_pk ${searchengines_options.omssa.omssa_search.omssa_single_window_pk}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
242 -omssa_double_window_pk ${searchengines_options.omssa.omssa_search.omssa_double_window_pk}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
243 -omssa_min_ann_int_pks ${searchengines_options.omssa.omssa_search.omssa_min_ann_int_pks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
244 -omssa_min_annotated_peaks ${searchengines_options.omssa.omssa_search.omssa_min_annotated_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
245 -omssa_max_ladders ${searchengines_options.omssa.omssa_search.omssa_max_ladders}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
246 -omssa_max_frag_charge ${searchengines_options.omssa.omssa_search.omssa_max_frag_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
247 -omssa_charge ${searchengines_options.omssa.omssa_search.omssa_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
248 -omssa_forward ${searchengines_options.omssa.omssa_search.omssa_forward}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
249 -omssa_rewind ${searchengines_options.omssa.omssa_search.omssa_rewind}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
250 -omssa_max_frag_series ${searchengines_options.omssa.omssa_search.omssa_max_frag_series}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
251 -omssa_corr ${searchengines_options.omssa.omssa_search.omssa_corr}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
252 -omssa_consecutive_p ${searchengines_options.omssa.omssa_search.omssa_consecutive_p}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
253 -omssa_hitlist_charge ${searchengines_options.omssa.omssa_search.omssa_hitlist_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
254 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
255
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
256 ## Iterative Search
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
257 #if $searchengines_options.omssa.omssa_isearch.omssa_isearch_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
258 -omssa_it_sequence_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_sequence_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
259 -omssa_it_spectrum_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_spectrum_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
260 -omssa_it_replace_evalue ${searchengines_options.omssa.omssa_isearch.omssa_it_replace_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
261 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
262
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
263 ## Semi-enzymatic
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
264 #if $searchengines_options.omssa.omssa_senzymatic.omssa_senzymatic_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
265 -omssa_min_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
266 -omssa_max_pep_length ${searchengines_options.omssa.omssa_senzymatic.omssa_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
267 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
268
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
269 ## Output
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
270 #if $searchengines_options.omssa.omssa_output_conditional.omssa_output_conditional_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
271 -omssa_max_evalue ${searchengines_options.omssa.omssa_output_conditional.omssa_max_evalue}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
272 -omssa_hitlist_length ${searchengines_options.omssa.omssa_output_conditional.omssa_hitlist_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
273 -omssa_format ${searchengines_options.omssa.omssa_output_conditional.omssa_format}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
274 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
275 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
276
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
277
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
278 ## COMET ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
279
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
280 #if $searchengines_options.comet.comet_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
281
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
282 #if $searchengines_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
283 -comet_min_peaks ${searchengines_options.comet.comet_spectrum.comet_min_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
284 -comet_min_peak_int ${searchengines_options.comet.comet_spectrum.comet_min_peak_int}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
285 -comet_remove_prec ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
286 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
287 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
288 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
289 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
290 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
291 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
292 #if $searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "3"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
293 -comet_remove_prec_tol ${searchengines_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
294 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
295 -comet_clear_mz_range_lower ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_lower}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
296 -comet_clear_mz_range_upper ${searchengines_options.comet.comet_spectrum.comet_clear_mz_range_upper}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
297 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
298
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
299 #if $searchengines_options.comet.comet_search.comet_search_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
300 -comet_enzyme_type ${searchengines_options.comet.comet_search.comet_enzyme_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
301 -comet_isotope_correction ${searchengines_options.comet.comet_search.comet_isotope_correction}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
302 -comet_min_prec_mass ${searchengines_options.comet.comet_search.comet_min_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
303 -comet_max_prec_mass ${searchengines_options.comet.comet_search.comet_max_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
304 -comet_max_frag_charge ${searchengines_options.comet.comet_search.comet_max_frag_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
305 -comet_remove_meth ${searchengines_options.comet.comet_search.comet_remove_meth}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
306 -comet_batch_size ${searchengines_options.comet.comet_search.comet_batch_size}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
307 -comet_num_ptms ${searchengines_options.comet.comet_search.comet_num_ptms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
308 -comet_req_ptms ${searchengines_options.comet.comet_search.comet_req_ptms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
309 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
310
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
311 #if $searchengines_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
312 -comet_theoretical_fragment_ions ${searchengines_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
313 -comet_frag_bin_offset ${searchengines_options.comet.comet_fragment_ions.comet_frag_bin_offset}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
314 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
315
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
316 #if $searchengines_options.comet.comet_output.comet_output_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
317 -comet_num_matches ${searchengines_options.comet.comet_output.comet_num_matches}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
318 -comet_output ${searchengines_options.comet.comet_output.comet_output_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
319 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
320 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
321
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
322
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
323 ## TIDE ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
324
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
325 #if $searchengines_options.tide.tide_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
326 ## Index parameters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
327 #if $searchengines_options.tide.tide_index.tide_index_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
328 -tide_min_pep_length ${searchengines_options.tide.tide_index.tide_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
329 -tide_max_pep_length ${searchengines_options.tide.tide_index.tide_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
330 -tide_min_prec_mass ${searchengines_options.tide.tide_index.tide_min_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
331 -tide_max_prec_mass ${searchengines_options.tide.tide_index.tide_max_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
332 -tide_monoisotopic ${searchengines_options.tide.tide_index.tide_monoisotopic}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
333 -tide_clip_n_term ${searchengines_options.tide.tide_index.tide_clip_n_term}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
334 #if str($searchengines_options.tide.tide_index.tide_num_ptms).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
335 -tide_num_ptms ${searchengines_options.tide.tide_index.tide_num_ptms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
336 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
337 -tide_num_ptms_per_type ${searchengines_options.tide.tide_index.tide_num_ptms_per_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
338 -tide_digestion_type ${searchengines_options.tide.tide_index.tide_digestion_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
339 -tide_print_peptides ${searchengines_options.tide.tide_index.tide_print_peptides}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
340 -tide_decoy_format ${searchengines_options.tide.tide_index.tide_decoy_format}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
341 -tide_keep_terminals ${searchengines_options.tide.tide_index.tide_keep_terminals}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
342 -tide_decoy_seed ${searchengines_options.tide.tide_index.tide_decoy_seed}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
343 -tide_remove_temp ${searchengines_options.tide.tide_index.tide_remove_temp}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
344 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
345
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
346 ## Search parameters
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
347 #if $searchengines_options.tide.tide_search.tide_search_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
348 -tide_compute_p ${searchengines_options.tide.tide_search.tide_compute_p}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
349 -tide_compute_sp ${searchengines_options.tide.tide_search.tide_compute_sp}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
350 -tide_min_spectrum_mz ${searchengines_options.tide.tide_search.tide_min_spectrum_mz}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
351 #if str($searchengines_options.tide.tide_search.tide_max_spectrum_mz).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
352 -tide_max_spectrum_mz ${searchengines_options.tide.tide_search.tide_max_spectrum_mz}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
353 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
354 -tide_min_spectrum_peaks ${searchengines_options.tide.tide_search.tide_min_spectrum_peaks}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
355 -tide_spectrum_charges ${searchengines_options.tide.tide_search.tide_spectrum_charges}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
356 -tide_remove_prec ${searchengines_options.tide.tide_search.tide_remove_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
357 -tide_remove_prec_tol ${searchengines_options.tide.tide_search.tide_remove_prec_tol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
358 -tide_use_flanking ${searchengines_options.tide.tide_search.tide_use_flanking}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
359 -tide_use_neutral_losses ${searchengines_options.tide.tide_search.tide_use_neutral_losses}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
360 -tide_mz_bin_width ${searchengines_options.tide.tide_search.tide_mz_bin_width}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
361 -tide_mz_bin_offset ${searchengines_options.tide.tide_search.tide_mz_bin_offset}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
362 -tide_max_psms ${searchengines_options.tide.tide_search.tide_max_psms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
363
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
364 #set $format_list = str($searchengines_options.tide.tide_search.tide_export).split(',')
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
365 #set $formats_available = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
366 #for $format_available in $formats_available:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
367 #if $format_available in $format_list:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
368 -$format_available 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
369 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
370 -$format_available 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
371 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
372 #end for
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
373 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
374 -tide_output_folder ${searchengines_options.tide.tide_output_folder}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
375 -tide_verbosity ${searchengines_options.tide.tide_verbosity}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
376 -tide_progress_indicator ${searchengines_options.tide.tide_progress_indicator}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
377 -tide_concat ${searchengines_options.tide.tide_concat}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
378 #if str($searchengines_options.tide.tide_store_spectra).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
379 -tide_store_spectra ${searchengines_options.tide.tide_store_spectra}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
380 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
381
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
382 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
383
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
384
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
385 ## DIRECTTAG ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
386
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
387 #if $searchengines_options.directtag.directtag_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
388 -directag_tag_length ${searchengines_options.directtag.directag_tag_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
389 -directag_max_var_mods ${searchengines_options.directtag.directag_max_var_mods}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
390 -directag_charge_states ${searchengines_options.directtag.directag_charge_states}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
391 -directag_duplicate_spectra ${searchengines_options.directtag.directag_duplicate_spectra}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
392 -directag_isotope_tolerance ${searchengines_options.directtag.directag_isotope_tolerance}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
393 -directag_deisotoping ${searchengines_options.directtag.directag_deisotoping}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
394 -directag_intensity_classes ${searchengines_options.directtag.directag_intensity_classes}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
395 #if str($searchengines_options.directtag.directag_output_suffix).strip() != '':
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
396 -directag_output_suffix ${searchengines_options.directtag.directag_output_suffix}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
397 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
398 -directag_max_peak_count ${searchengines_options.directtag.directag_max_peak_count}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
399 -directag_max_tag_count ${searchengines_options.directtag.directag_max_tag_count}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
400 -directag_tic_cutoff ${searchengines_options.directtag.directag_tic_cutoff}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
401 -directag_complement_tolerance ${searchengines_options.directtag.directag_complement_tolerance}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
402 -directag_adjustment_step ${searchengines_options.directtag.directag_adjustment_step}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
403 -directag_min_adjustment ${searchengines_options.directtag.directag_min_adjustment}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
404 -directag_max_adjustment ${searchengines_options.directtag.directag_max_adjustment}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
405 -directag_intensity_weight ${searchengines_options.directtag.directag_intensity_weight}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
406 -directag_fidelity_weight ${searchengines_options.directtag.directag_fidelity_weight}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
407 -directag_complement_weight ${searchengines_options.directtag.directag_complement_weight}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
408 -directag_adjust_precursor ${searchengines_options.directtag.directag_adjust_precursor}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
409 -directag_ms_charge_state ${searchengines_options.directtag.directag_ms_charge_state}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
410 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
411
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
412 ## METAMORPHEUS ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
413
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
414 #if $searchengines_options.metamorpheus.metamorpheus_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
415 ## Search options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
416 #if $searchengines_options.metamorpheus.metamorpheus_search.metamorpheus_search_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
417 -meta_morpheus_search_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_search_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
418 -meta_morpheus_num_partitions ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_num_partitions}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
419 -meta_morpheus_dissociation_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_dissociation_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
420 -meta_morpheus_max_mods_for_peptide ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_mods_for_peptide}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
421 -meta_morpheus_score_cutoff ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_score_cutoff}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
422 -meta_morpheus_use_delta_score ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_use_delta_score}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
423 -meta_morpheus_mass_diff_acceptor_type ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_mass_diff_acceptor_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
424 -meta_morpheus_min_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_min_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
425 -meta_morpheus_max_pep_length ${searchengines_options.metamorpheus.metamorpheus_search.meta_morpheus_max_pep_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
426 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
427
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
428 ## Output options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
429 #if $searchengines_options.metamorpheus.metamorpheus_output.metamorpheus_output_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
430 -meta_morpheus_write_mzid ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_mzid}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
431 -meta_morpheus_write_pepxml ${searchengines_options.metamorpheus.metamorpheus_output.meta_morpheus_write_pepxml}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
432 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
433
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
434 ## Deisotoping options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
435 #if $searchengines_options.metamorpheus.metamorpheus_deisotoping.metamorpheus_deisotoping_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
436 -meta_morpheus_use_provided_prec ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_use_provided_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
437 -meta_morpheus_do_prec_deconv ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_do_prec_deconv}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
438 -meta_morpheus_deconv_int_ratio ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_int_ratio}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
439 -meta_morpheus_deconv_mass_tol ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
440 -meta_morpheus_deconv_mass_tol_type ${searchengines_options.metamorpheus.metamorpheus_deisotoping.meta_morpheus_deconv_mass_tol_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
441 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
442
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
443 ## Protein grouping options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
444 #if $searchengines_options.metamorpheus.metamorpheus_proteingrouping.metamorpheus_proteingrouping_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
445 -meta_morpheus_mod_peptides_are_different ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_mod_peptides_are_different}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
446 -meta_morpheus_no_one_hit_wonders ${searchengines_options.metamorpheus.metamorpheus_proteingrouping.meta_morpheus_no_one_hit_wonders}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
447 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
448
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
449 ## Peak trimming options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
450 #if $searchengines_options.metamorpheus.metamorpheus_peaktrimming.metamorpheus_peaktrimming_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
451 -meta_morpheus_trim_ms1 ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_ms1}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
452 -meta_morpheus_trim_msms ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_trim_msms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
453 -meta_morpheus_num_peaks_per_window ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_peaks_per_window}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
454 -meta_morpheus_min_allowed_int_ratio_to_base_peak ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_min_allowed_int_ratio_to_base_peak}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
455 -meta_morpheus_window_with_thompson ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_window_with_thompson}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
456 -meta_morpheus_num_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_num_windows}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
457 -meta_morpheus_norm_across_all_windows ${searchengines_options.metamorpheus.metamorpheus_peaktrimming.meta_morpheus_norm_across_all_windows}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
458 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
459
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
460 ## Silico digestion related options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
461 #if $searchengines_options.metamorpheus.metamorpheus_silico.metamorpheus_silico_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
462 -meta_morpheus_frag_term ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_frag_term}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
463 -meta_morpheus_max_frag_size ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_frag_size}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
464 -meta_morpheus_search_target ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_search_target}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
465 -meta_morpheus_decoy_type ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_decoy_type}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
466 -meta_morpheus_max_mod_isoforms ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_max_mod_isoforms}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
467 -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
468 -meta_morpheus_min_variant_depth ${searchengines_options.metamorpheus.metamorpheus_silico.meta_morpheus_min_variant_depth}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
469 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
470
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
471 ## G-PTM search related options
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
472 #if $searchengines_options.metamorpheus.metamorpheus_gptm.metamorpheus_gptm_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
473 -meta_morpheus_gptm ${searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
474
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
475 ## Need to transform the list of gptm acronyms to real gptm values for SearchGUI
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
476 #if str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != "None" and str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories) != ""
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
477 #set $meta_morpheus_gptm_categories_list = set(str($searchengines_options.metamorpheus.metamorpheus_gptm.meta_morpheus_gptm_categories).split(','))
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
478 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
479 #set $meta_morpheus_gptm_categories_list = set()
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
480 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
481 #set $meta_morpheus_categories_mapping = {'common_fixed_variable': 'Common Fixed and Variable', 'common_biological': 'Common Biological','common_artifact': 'Common Artifact', 'metal': 'Metal','less_common': 'Less Common','labeling': 'Labeling','subs_1n': 'Substitution (1 Nucleotide)','subs_2n': 'Substitution (2+ Nucleotides)','other': 'Other'}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
482 #set $meta_morpheus_gptm_real_categories_list = []
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
483 #for $meta_morpheus_gptm_category_item in $meta_morpheus_gptm_categories_list:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
484 $meta_morpheus_gptm_real_categories_list.append("'"+$meta_morpheus_categories_mapping[$meta_morpheus_gptm_category_item]+"'")
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
485 #end for
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
486
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
487 #if len($meta_morpheus_gptm_real_categories_list) > 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
488 -meta_morpheus_gptm_categories #echo ','.join($meta_morpheus_gptm_real_categories_list)#
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
489 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
490
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
491 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
492
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
493 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
494
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
495 ## NOVOR ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
496
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
497 #if $searchengines_options.novor.novor_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
498 -novor_fragmentation ${searchengines_options.novor.novor_fragmentation}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
499 -novor_mass_analyzer ${searchengines_options.novor.novor_mass_analyzer}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
500 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
501
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
502
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
503 ## PEPNOVO+ ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
504
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
505 #if $searchengines_options.pepnovo.pepnovo_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
506 -pepnovo_hitlist_length ${searchengines_options.pepnovo.pepnovo_hitlist_length}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
507 -pepnovo_estimate_charge ${searchengines_options.pepnovo.pepnovo_estimate_charge}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
508 -pepnovo_correct_prec_mass ${searchengines_options.pepnovo.pepnovo_correct_prec_mass}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
509 -pepnovo_discard_spectra ${searchengines_options.pepnovo.pepnovo_discard_spectra}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
510 -pepnovo_generate_blast ${searchengines_options.pepnovo.pepnovo_generate_blast}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
511 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
512
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
513
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
514 ## PNOVO+ ADVANCED SETTINGS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
515
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
516 #if $searchengines_options.pnovo.pnovo_advanced == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
517 -pnovo_num_peptides ${searchengines_options.pnovo.pnovo_num_peptides}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
518 -pnovo_lower_prec ${searchengines_options.pnovo.pnovo_lower_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
519 -pnovo_upper_prec ${searchengines_options.pnovo.pnovo_upper_prec}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
520 -pnovo_activation ${searchengines_options.pnovo.pnovo_activation}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
521 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
522
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
523
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
524 ## -- ADVANCED PARAMETERS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
525
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
526 ## SPECTRUM ANNOTATION
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
527 -annotation_level $advanced_options.spectrum_annotation_options.annotation_level
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
528
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
529 ## if the user modifies fragment_tol but he does not modify annotation_mz_tolerance,
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
530 ## we must overwrite default annotation_mz_tolerance value with fragment_tol value
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
531
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
532 #if not ($spectrum_matching_options.fragment_tol != 0.5 and $advanced_options.spectrum_annotation_options.annotation_mz_tolerance == 0.5)
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
533 -annotation_mz_tolerance $advanced_options.spectrum_annotation_options.annotation_mz_tolerance
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
534 #end if
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
535 -annotation_high_resolution $advanced_options.spectrum_annotation_options.annotation_high_resolution
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
536 ## TODO: There are still many options from the GUI to be incorporated to the CLI
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
537
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
538
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
539 ## SEQUENCE MATCHING
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
540 -sequence_matching_type $advanced_options.sequence_matching_options.sequence_matching_type
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
541 -sequence_matching_x $advanced_options.sequence_matching_options.sequence_matching_x
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
542 -sequence_matching_enzymatic_tags $advanced_options.sequence_matching_options.sequence_matching_enzymatic_tags
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
543 -sequence_matching_max_ptms_per_tag $advanced_options.sequence_matching_options.sequence_matching_max_ptms_per_tag
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
544 -sequence_matching_min_amino_acid_score $advanced_options.sequence_matching_options.sequence_matching_min_amino_acid_score
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
545 -sequence_matching_min_tag_length $advanced_options.sequence_matching_options.sequence_matching_min_tag_length
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
546
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
547
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
548 ## IMPORT FILTERS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
549
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
550 -import_peptide_length_min '${advanced_options.import_filters_options.min_peptide_length}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
551 -import_peptide_length_max '${advanced_options.import_filters_options.max_peptide_length}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
552 -import_precursor_mz '${advanced_options.import_filters_options.max_precursor_error}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
553 -import_precursor_mz_ppm '${advanced_options.import_filters_options.max_precursor_error_type}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
554 #if $advanced_options.import_filters_options.missed_cleavages_min
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
555 -import_missed_cleavages_min '${advanced_options.import_filters_options.missed_cleavages_min}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
556 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
557 #if $advanced_options.import_filters_options.missed_cleavages_max
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
558 -import_missed_cleavages_max '${advanced_options.import_filters_options.missed_cleavages_max}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
559 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
560 -exclude_unknown_ptms '${advanced_options.import_filters_options.exclude_unknown_ptms}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
561
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
562
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
563 ## PTM LOCALIZATION
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
564
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
565 -ptm_score '${advanced_options.ptm_localization_options.ptm_score.ptm_score_selector}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
566 #if $advanced_options.ptm_localization_options.ptm_score.ptm_score_selector == 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
567 -score_neutral_losses '${advanced_options.ptm_localization_options.ptm_score.neutral_losses}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
568 #if str($advanced_options.ptm_localization_options.ptm_score.ptm_threshold) != ''
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
569 -ptm_threshold '${advanced_options.ptm_localization_options.ptm_score.ptm_threshold}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
570 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
571 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
572 -ptm_alignment '${advanced_options.ptm_localization_options.ptm_alignment}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
573 -ptm_sequence_matching_type '${advanced_options.ptm_localization_options.ptm_sequence_matching_type}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
574
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
575
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
576 ## GENE ANNOTATION
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
577
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
578 $advanced_options.gene_annotation_options.use_gene_mapping
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
579 #if $advanced_options.gene_annotation_options.use_gene_mapping:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
580 $advanced_options.gene_annotation_options.update_gene_mapping
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
581 #else:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
582 -updateGeneMapping 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
583 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
584
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
585
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
586 ## PROTEIN INFERENCE
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
587
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
588 #if $advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
589 -simplify_groups 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
590 -simplify_evidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_evidence}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
591 -simplify_confidence ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
592 -simplify_confidence_threshold ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_confidence_threshold}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
593 -simplify_enzymaticity ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_enzymaticity}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
594 -simplify_variant ${advanced_options.protein_inference_options.simplify_protein_groups_conditional.simplify_protein_groups_variant}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
595 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
596 -simplify_groups 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
597 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
598 -pi_modifications ${advanced_options.protein_inference_options.simplify_protein_pi_modifications}
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
599
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
600
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
601
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
602
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
603 ## VALIDATION LEVELS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
604
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
605 -protein_fdr '${advanced_options.validation_levels_options.protein_fdr}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
606 -peptide_fdr '${advanced_options.validation_levels_options.peptide_fdr}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
607 -psm_fdr '${advanced_options.validation_levels_options.psm_fdr}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
608
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
609
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
610 ## FRACTION ANALYSIS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
611
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
612 -protein_fraction_mw_confidence '${advanced_options.fraction_analysis_options.protein_fraction_mw_confidence}'
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
613
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
614
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
615
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
616 ## DATABASE PROCESSING OPTIONS
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
617
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
618 #if $advanced_options.database_processing_options.decoy_conditional.create_decoy_selector == "yes"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
619 -fasta_target_decoy 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
620 -fasta_decoy_tag $advanced_options.database_processing_options.decoy_conditional.decoy_tag
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
621 -fasta_decoy_type $advanced_options.database_processing_options.decoy_conditional.decoy_type
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
622 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
623 -fasta_target_decoy 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
624 -fasta_decoy_file_tag $advanced_options.database_processing_options.decoy_file_tag
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
625 ]]>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
626 </command>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
627 <inputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
628
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
629
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
630 <!-- SPECTRUM MATCHING PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
631
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
632 <section name="spectrum_matching_options" expanded="false" title="Spectrum Matching Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
633
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
634 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
635 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
636 <expand macro="modifications"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
637 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
638 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
639 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
640 <expand macro="modifications"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
641 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
642
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
643 <conditional name="digestion">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
644 <param name="cleavage" type="select" label="Digestion">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
645 <option value="0">Select Enzymes</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
646 <option value="1">Unspecific Cleavage</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
647 <option value="2">Whole Protein</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
648 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
649 <when value="0">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
650 <repeat name="digests" min="1" title="Enzymes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
651 <param name="enzyme" type="select" label="Enzyme"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
652 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
653 <option value="Trypsin">Trypsin</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
654 <option value="Trypsin (no P rule)">Trypsin (no P rule)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
655 <option value="Arg-C">Arg-C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
656 <option value="Arg-C (no P rule)">Arg-C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
657 <option value="Arg-N">Arg-N</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
658 <option value="Glu-C">Glu-C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
659 <option value="Lys-C">Lys-C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
660 <option value="Lys-C (no P rule)">Lys-C (no P rule)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
661 <option value="Lys-N">Lys-N</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
662 <option value="Asp-N">Asp-N</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
663 <option value="Asp-N (ambic)">Asp-N (ambic)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
664 <option value="Chymotrypsin">Chymotrypsin</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
665 <option value="Chymotrypsin (no P rule)">Chymotrypsin (no P rule)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
666 <option value="Pepsin A">Pepsin A</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
667 <option value="CNBr">CNBr</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
668 <option value="Thermolysin">Thermolysin</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
669 <option value="LysargiNase">LysargiNase</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
670 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
671 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
672 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
673
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
674 <param name="specificity" type="select" label="Specificity">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
675 <option value="0" selected="true">Specific at both termini</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
676 <option value="1">Semi-Specific - one terminus</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
677 <option value="2">Specific at the N-terminus only</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
678 <option value="3">Specific at the C-terminus only</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
679 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
680
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
681 </repeat>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
682 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
683 <when value="1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
684 <when value="2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
685 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
686
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
687 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
688 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
689 <option value="1">Parts per million (ppm)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
690 <option value="0">Daltons</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
691 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
692 <param name="precursor_ion_tol" type="float" value="10" label="Precursor Ion Tolerance"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
693 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
694 <param name="fragment_tol_units" type="select" label="Fragment Tolerance Units"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
695 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
696 <option value="1">Parts per million (ppm)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
697 <option value="0" selected="true">Daltons</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
698 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
699 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
700 help="Provide error value for fragment ions, based on instrument used"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
701 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
702 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
703 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
704 <option value="a">a</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
705 <option value="b" selected="true">b</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
706 <option value="c">c</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
707 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
708 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
709 <option value="x">x</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
710 <option value="y" selected="true">y</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
711 <option value="z">z</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
712 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
713 <param name="min_isotope" label="Minimum precursor isotope" type="integer" value="0" help="default: 0" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
714 <param name="max_isotope" label="Maximum precursor isotope" type="integer" value="1" help="default: 1" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
715 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
716
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
717
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
718 <!-- - SEARCH ENGINES OPTIONS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
719
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
720 <section name="searchengines_options" expanded="false" title="Search Engines Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
721
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
722 <!-- X!TANDEM ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
723 <conditional name="xtandem">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
724 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
725 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
726 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
727 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
728 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
729 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
730 <!-- Spectrum Import -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
731 <conditional name="xtandem_spectrum">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
732 <param name="xtandem_spectrum_selector" type="select" label="X!Tandem: Spectrum Import Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
733 <option value="yes" selected="True">Set Spectrum Import Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
734 <option value="no">Keep Default Spectrum Import Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
735 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
736 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
737 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
738 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
739 label="X!Tandem: Dynamic Range" value="100" type="integer" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
740 <param name="xtandem_npeaks" type="integer" value="50"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
741 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
742 <param name="xtandem_min_frag_mz" type="integer" value="200"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
743 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
744 <param name="xtandem_min_peaks" type="integer" value="5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
745 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
746 <param name="xtandem_noise_suppr" type="boolean" checked="false" truevalue="1" falsevalue="0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
747 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
748 <param name="xtandem_min_prec_mass" type="integer" value="500"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
749 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
750 <param name="xtandem_parent_isotope_correction" type="boolean" checked="true" truevalue="1" falsevalue="0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
751 label="X!Tandem: Parent monoisotopic mass isotope error" help="when activated, the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide. "/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
752 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
753 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
754 <!-- Advanced search -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
755 <conditional name="xtandem_asearch">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
756 <param name="xtandem_asearch_selector" type="select" label="X!Tandem: Advanced Search Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
757 <option value="yes">Set Advanced Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
758 <option value="no" selected="True">Keep Default Advanced Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
759 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
760 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
761 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
762 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
763 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
764 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
765 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
766 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
767 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
768 <param name="xtandem_ptm_complexity" type="float" value="6.0" help="maximum number of variable modification alternatives that will be tested for a particular peptide"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
769 label="X!Tandem: PTM complexity" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
770 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
771 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
772 <!-- Output -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
773 <conditional name="xtandem_output">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
774 <param name="xtandem_output_selector" type="select" label="X!Tandem: Output Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
775 <option value="yes">Set Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
776 <option value="no" selected="True">Keep Default Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
777 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
778 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
779 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
780 <conditional name="xtandem_output_results_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
781 <param name="xtandem_output_results_selector" type="select" label="" help="Determines which results are written to the output file at the end of a modelling session">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
782 <option value="all" selected="True">All</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
783 <option value="valid" >Valid</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
784 <option value="stochastic" >Stochastic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
785 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
786 <when value="all"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
787 <when value="valid">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
788 <param name="xtandem_evalue" help="Highest value for recorded peptides"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
789 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
790 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
791 <when value="stochastic">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
792 <param name="xtandem_evalue" help="Highest value for recorded peptides"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
793 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
794 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
795 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
796
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
797 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
798 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
799 <param name="xtandem_output_sequences" help="Controls output of sequence information"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
800 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
801 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
802 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
803 <param name="xtandem_output_histograms" help="Controls output of statistical information about an spectrum-to-sequence assignment"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
804 label="X!Tandem: Output Histograms" type="boolean" truevalue="1" falsevalue="0" checked="false" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
805 <!-- TODO: Integration with Skyline not ready yet
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
806 <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
807 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
808 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
809
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
810 <!-- Refine -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
811 <conditional name="xtandem_refine">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
812 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
813 <option value="no">Don't refine</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
814 <option value="yes" selected="True">Use refinement</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
815 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
816 <when value="no"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
817 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
818 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
819 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
820 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
821 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
822 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
823 label="X!Tandem: semi-enzymatic cleavage, refinement" help="Search for semi-tryptic peptides during refinement"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
824 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
825 label="X!Tandem: Use potential modifications for full refinement" help="Controls the use of refinement modifications in all refinement modules."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
826 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
827 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
828 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
829 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
830 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
831 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
832 <!-- TODO: Refinement modifications when implemented in the command line -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
833 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
834 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
835 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
836 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
837
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
838
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
839 <!-- MyriMatch ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
840 <conditional name="myrimatch">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
841 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
842 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
843 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
844 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
845 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
846 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
847 <param name="myrimatch_min_pep_length" type="integer" value="6"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
848 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
849 <param name="myrimatch_max_pep_length" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
850 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
851 <param name="myrimatch_min_prec_mass" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
852 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
853 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
854 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
855 <param name="myrimatch_num_matches" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
856 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
857 <param name="myrimatch_num_ptms" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
858 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
859
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
860 <!-- TODO : TO BE UPDATED WHEN CLI DOES. TO CONFIRM MANUAL OPTION FIRSTLY -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
861 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
862 <option value="CID" selected="True">CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
863 <option value="HCD" >HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
864 <option value="ETD" >ETD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
865 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
866 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
867 <option value="0">non-tryptic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
868 <option value="1">semi-tryptic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
869 <option value="2" selected="True" >fully-tryptic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
870 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
871 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
872 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
873 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
874 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
875 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
876 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
877 <param name="myrimatch_intensity_classes" type="integer" value="3"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
878 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
879 <param name="myrimatch_class_multiplier" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
880 label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
881 <param name="myrimatch_num_batches" type="integer" value="50"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
882 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
883 <param name="myrimatch_max_peak" type="integer" value="100"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
884 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
885 <param name="myrimatch_output" type="select" label="MyriMatch: output format option">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
886 <option value="mzIdentML" selected="True" >mzIdentML</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
887 <option value="pepXML">pepXML</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
888 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
889 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
890 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
891
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
892 <!-- MS-GF+ ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
893 <conditional name="msgf">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
894 <param name="msgf_advanced" type="select" label="MSGF Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
895 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
896 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
897 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
898 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
899 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
900 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
901 label="MSGF: Search Decoy Database" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
902 <param name="msgf_instrument" label="MSGF: MS/MS Detector" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
903 <option value="0" >Low-res LCQ/LTQ</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
904 <option value="1" >Orbitrap/FTICR</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
905 <option value="2" >TOF</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
906 <option value="3" selected="True">Q-Exactive</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
907 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
908 <param name="msgf_fragmentation" label="MSGF: Fragmentation method" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
909 <option value="0" >As written in the spectrum or CID if no info</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
910 <option value="1" >CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
911 <option value="2" >ETD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
912 <option value="3" selected="True">HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
913 <option value="4" >UVPD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
914 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
915 <param name="msgf_protocol" label="MSGF: Protocol" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
916 <option value="0" selected="True">Automatic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
917 <option value="1" >Phosphorylation</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
918 <option value="2" >iTRAQ</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
919 <option value="3" >iTRAQPhospho</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
920 <option value="4" >TMT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
921 <option value="5" >Standard</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
922 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
923 <param name="msgf_termini" type="select" format="txt"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
924 label="MSGF: Enzymatic Terminals" help="Searches will take much longer if selecting a value other than 2">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
925 <option value="0">None required</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
926 <option value="1">At least one</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
927 <option value="2" selected="true">Both</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
928 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
929 <param name="msgf_min_pep_length" type="integer" value="8"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
930 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
931 <param name="msgf_max_pep_length" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
932 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
933 <param name="msgf_num_ptms" label="MSGF: Max Variable PTMs per Peptide" type="integer" value="2"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
934 <param name="msgf_num_matches" label="MSGF: Number of Spectrum Matches" type="integer" value="10" help="Number of peptide matches per spectrum to report" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
935 <param name="msgf_additional" label="MS-GF+ additional Output" type="select" help="Additional features to export">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
936 <option value="0" selected="True">output basic scores only</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
937 <option value="1" >output additional features</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
938 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
939 <conditional name="msgf_tasks">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
940 <param name="msgf_tasks_custom" type="select" label="Number of tasks to use on the threads">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
941 <option value="yes">Custom</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
942 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
943 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
944 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
945 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
946 <param name="msgf_num_tasks" type="integer" value="4"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
947 label="MSGF: Custom number of tasks to use on the threads"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
948 help="Manually set the number of tasks to create for the search. More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). Check the documentation carefully. "/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
949 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
950 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
951 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
952 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
953
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
954 <!-- MS-AMANDA ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
955 <conditional name="ms_amanda">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
956 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
957 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
958 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
959 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
960 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
961 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
962 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
963 label="MS Amanda: Generate Decoys" help="generate decoys" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
964 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
965 help="MS Amanda instrument id option. Available ion types are listed here.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
966
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
967 <option value="b, y" selected="True">b, y</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
968 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
969 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
970 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
971 <option value="a, b, y" >a, b, y</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
972 <option value="a, b, y, Imm" >a, b, y, Imm</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
973 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
974 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
975 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
976 <option value="b, y, INT" >b, y, INT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
977 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
978 <option value="a, b, y, INT" >a, b, y, INT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
979 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
980 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
981 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
982 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
983
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
984 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
985 <param name="ms_amanda_max_rank" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
986 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
987 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
988 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
989 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
990 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
991
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
992 <!-- OMSSA ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
993 <conditional name="omssa">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
994 <param name="omssa_advanced" type="select" label="OMSSA Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
995 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
996 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
997 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
998 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
999 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1000 <!-- Spectrum -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1001 <conditional name="omssa_spectrum">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1002 <param name="omssa_spectrum_selector" type="select" label="OMSSA: Spectrum Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1003 <option value="yes" selected="True">Set Spectrum Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1004 <option value="no">Keep Default Spectrum Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1005 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1006 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1007 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1008 <param name="omssa_low_intensity" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1009 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1010 <param name="omssa_high_intensity" type="float" value="0.2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1011 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1012 <param name="omssa_intensity_incr" type="float" value="0.0005"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1013 label="OMSSA: Intensity Increment" help="Intensity increment" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1014 <param name="omssa_min_peaks" type="integer" value="4"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1015 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1016 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1017 label="OMSSA: Remove precursors" help="Eliminate charge reduced precursors in spectra" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1018 <param name="omssa_estimate_charge" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1019 label="OMSSA: Estimate charge" help="estimate precursor charge" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1020 <option value="0" >Believe input file</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1021 <option value="1" selected="True">Use range</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1022 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1023 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1024 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1025 <param name="omssa_fraction" type="float" value="0.95"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1026 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1027 <param name="omssa_prec_per_spectrum" type="integer" value="1"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1028 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1029 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1030 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1031 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1032 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1033 <!-- Database -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1034 <conditional name="omssa_database">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1035 <param name="omssa_database_selector" type="select" label="OMSSA: Database Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1036 <option value="yes" >Set Database Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1037 <option value="no" selected="True">Keep Default Database Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1038 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1039 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1040 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1041 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1042 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1043 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1044 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1045 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1046 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1047 <!-- Search -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1048 <conditional name="omssa_search">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1049 <param name="omssa_search_selector" type="select" label="OMSSA: Search Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1050 <option value="yes">Set Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1051 <option value="no" selected="True">Keep Default Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1052 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1053 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1054 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1055 <!-- TODO: TO BE IMPLEMENTED IN THE CLI, MINIMUM PRECURSOR CHARGE FOR MULTIPLY CHARGED FRAGMENTS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1056 <param name="omssa_neutron" type="float" value="1446.94"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1057 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1058 <param name="omssa_single_window_wd" type="integer" value="27"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1059 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1060 <param name="omssa_double_window_wd" type="integer" value="14"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1061 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1062 <param name="omssa_single_window_pk" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1063 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1064 <param name="omssa_double_window_pk" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1065 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1066 <param name="omssa_min_ann_int_pks" type="integer" value="6"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1067 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1068 <param name="omssa_min_annotated_peaks" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1069 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1070 <param name="omssa_max_ladders" type="integer" value="128"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1071 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1072 <param name="omssa_max_frag_charge" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1073 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1074 <param name="omssa_charge" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1075 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1076 <option value="0" >Minus</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1077 <option value="1" selected="True">Plus</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1078 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1079 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1080 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1081 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1082 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1083 <param name="omssa_max_frag_series" type="integer" value="100"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1084 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1085 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1086 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1087 <param name="omssa_consecutive_p" type="float" value="0.5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1088 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1089 <param name="omssa_hitlist_charge" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1090 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1091 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1092 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1093 <!-- Iterative Search -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1094 <conditional name="omssa_isearch">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1095 <param name="omssa_isearch_selector" type="select" label="OMSSA: Iterative Search Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1096 <option value="yes" >Set Iterative Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1097 <option value="no" selected="True">Keep Default Iterative Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1098 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1099 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1100 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1101 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1102 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1103 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1104 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1105 <param name="omssa_it_replace_evalue" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1106 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search (0.0 means all)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1107 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1108 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1109
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1110 <!-- Semi-enzymatic -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1111 <conditional name="omssa_senzymatic">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1112 <param name="omssa_senzymatic_selector" type="select" label="OMSSA: Semi-enzymatic Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1113 <option value="yes" >Set Semi-enzymatic Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1114 <option value="no" selected="True">Keep Default Semi-enzymatic Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1115 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1116 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1117 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1118 <param name="omssa_min_pep_length" type="integer" value="8"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1119 label="OMSSA: Minimum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1120 <param name="omssa_max_pep_length" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1121 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1122 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1123 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1124
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1125 <!-- Output -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1126 <conditional name="omssa_output_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1127 <param name="omssa_output_conditional_selector" type="select" label="OMSSA: Output Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1128 <option value="yes">Set Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1129 <option value="no" selected="True">Keep Default Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1130 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1131 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1132 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1133 <param name="omssa_max_evalue" type="float" value="100"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1134 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1135 <param name="omssa_hitlist_length" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1136 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1137 <param name="omssa_format" label="OMSSA output format" type="select" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1138 <option value="0" selected="True">OMX</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1139 <option value="1" >CSV</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1140 <option value="2" >pepXML</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1141 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1142 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1143 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1144
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1145 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1146 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1147
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1148
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1149 <!-- Comet ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1150 <conditional name="comet">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1151 <param name="comet_advanced" type="select" label="Comet Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1152 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1153 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1154 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1155 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1156 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1157 <!-- Spectrum Related parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1158 <conditional name="comet_spectrum">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1159 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1160 <option value="yes" selected="True">Set Spectrum Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1161 <option value="no">Keep Default Spectrum Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1162 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1163 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1164 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1165 <param name="comet_min_peaks" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1166 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1167 <param name="comet_min_peak_int" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1168 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1169 <conditional name="comet_prec">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1170 <param name="comet_remove_prec" label="Comet: Remove Precursor peaks" type="select" help="Select for precursor m/z signal removal">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1171 <option value="0" selected="True" >no</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1172 <option value="1">yes</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1173 <option value="2">yes + charge reduced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1174 <option value="3">yes + phospate neutral</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1175 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1176 <when value="0" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1177 <when value="1">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1178 <param name="comet_remove_prec_tol" type="float" value="1.5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1179 label="Comet: Remove Precursor Tolerance" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1180 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1181 <when value="2">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1182 <param name="comet_remove_prec_tol" type="float" value="1.5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1183 label="Comet: Remove Precursor Tolerance" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1184 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1185 <when value="3">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1186 <param name="comet_remove_prec_tol" type="float" value="1.5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1187 label="Comet: Remove Precursor Tolerance" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1188 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1189 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1190 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1191 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1192 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1193 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1194 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1195 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1196 <!-- Search Related parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1197 <conditional name="comet_search">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1198 <param name="comet_search_selector" type="select" label="Comet: Search Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1199 <option value="yes">Set Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1200 <option value="no" selected="True">Keep Default Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1201 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1202 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1203 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1204 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1205 <option value="1">semi-specific</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1206 <option value="2" selected="True">full-enzyme</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1207 <option value="8">unspecific N-term</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1208 <option value="9">unspecific C-term</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1209 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1210 <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1211 <option value="0">off</option>
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
1212 <option value="1">0,+1</option>
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1213 <option value="2">0,+1,+2</option>
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
1214 <option value="3" selected="True">0,+1,+2,+3</option>
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1215 <option value="4">-8,-4,0,+4,+8</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1216 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1217 <param name="comet_min_prec_mass" type="float" value="600.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1218 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1219 <param name="comet_max_prec_mass" type="float" value="5000.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1220 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1221 <param name="comet_max_frag_charge" type="integer" value="3"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1222 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1223 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1224 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1225 <param name="comet_batch_size" type="integer" value="0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1226 label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1227 <param name="comet_num_ptms" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1228 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1229 <param name="comet_req_ptms" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1230 label="Comet: Require Variable PTMs" help="Require at least one variable PTM per peptide" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1231 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1232 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1233 <!-- Fragment Ions Related parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1234 <conditional name="comet_fragment_ions">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1235 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1236 <option value="yes">Set Fragment Ions Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1237 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1238 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1239 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1240 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1241 <param name="comet_theoretical_fragment_ions" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1242 label="Comet: Correlation Score type" help="Specifies how theoretical fragment ion peaks are represented (on the sum in the bin alone or using flanking bins too)">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1243 <option value="0" selected="True">Summed intensities + flanking</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1244 <option value="1">Summed intensities</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1245 </param>
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
1246 <param name="comet_frag_bin_offset" type="float" value="0"
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1247 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1248 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1249 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1250 <!-- Output Related parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1251 <conditional name="comet_output">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1252 <param name="comet_output_selector" type="select" label="Comet: Output Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1253 <option value="yes">Set Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1254 <option value="no" selected="True">Keep Default Output Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1255 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1256 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1257 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1258 <param name="comet_num_matches" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1259 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1260 <param name="comet_output_type" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1261 label="Comet: Output type" help="Output type: PepXML, SQT, TXT or Percolator">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1262 <option value="PepXML" selected="True">PepXML</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1263 <option value="SQT">SQT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1264 <option value="TXT">TXT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1265 <option value="Percolator">Percolator</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1266 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1267 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1268 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1269 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1270 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1271
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1272 <!-- TIDE ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1273 <conditional name="tide">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1274 <param name="tide_advanced" type="select" label="TIDE Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1275 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1276 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1277 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1278 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1279 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1280 <!-- Index parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1281 <conditional name="tide_index">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1282 <param name="tide_index_selector" type="select" label="Tide: Index Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1283 <option value="yes" selected="True">Set Index Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1284 <option value="no" >Keep Default Index Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1285 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1286 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1287 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1288 <param name="tide_min_pep_length" type="integer" value="6"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1289 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1290 <param name="tide_max_pep_length" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1291 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1292 <param name="tide_min_prec_mass" type="float" value="200.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1293 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1294 <param name="tide_max_prec_mass" type="float" value="7200.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1295 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1296 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1297 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1298 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1299 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1300 <param name="tide_num_ptms" type="integer" value="" optional="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1301 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1302 <param name="tide_num_ptms_per_type" type="integer" value="2"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1303 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1304 <param name="tide_digestion_type" label="TIDE: Enzyme/Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1305 <option value="full-digest" selected="True">full-digest</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1306 <option value="partial-digest" >partial-digest</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1307 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1308 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1309 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1310 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1311 <option value="none" selected="True">none</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1312 <option value="shuffle" >shuffle</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1313 <option value="peptide-revers" >peptide-reverse</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1314 <option value="protein-reverse" >protein-reverse</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1315 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1316 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1317 <option value="N" >N</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1318 <option value="C" >C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1319 <option value="NC" selected="True">NC</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1320 <option value="non" >none</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1321 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1322 <param name="tide_decoy_seed" type="integer" value="1"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1323 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1324 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1325 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1326 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1327 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1328
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1329 <!-- Search parameters -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1330 <conditional name="tide_search">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1331 <param name="tide_search_selector" type="select" label="Tide: Search Related">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1332 <option value="yes">Set Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1333 <option value="no" selected="True">Keep Default Search Parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1334 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1335 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1336 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1337 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1338 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1339 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1340 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1341 <param name="tide_min_spectrum_mz" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1342 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1343 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1344 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1345 <param name="tide_min_spectrum_peaks" type="integer" value="20"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1346 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1347 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1348 <option value="1" >1</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1349 <option value="2" >2</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1350 <option value="3" >3</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1351 <option value="all" selected="True">all</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1352 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1353 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1354 label="TIDE: Remove Precursor Peak" help="If true, the peak that corresponds to the precursor mass is excluded"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1355 <param name="tide_remove_prec_tol" type="float" value="1.5"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1356 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1357 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1358 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1359 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1360 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1361 <param name="tide_mz_bin_width" type="float" value="0.02"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1362 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1363 <param name="tide_mz_bin_offset" type="float" value="0.0"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1364 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1365 <param name="tide_max_psms" type="integer" value="10"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1366 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1367 <param name="tide_export" label="TIDE: Output Format" type="select" multiple="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1368 display="checkboxes" help="Choose the output format">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1369 <option value="tide_export_text" selected="True">Text</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1370 <option value="tide_export_sqt" >SQT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1371 <option value="tide_export_pepxml" >pepxml</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1372 <option value="tide_export_mzid" >MzIdentML</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1373 <option value="tide_export_pin" >Percolator input file</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1374 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1375 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1376 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1377
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1378 <!-- other options -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1379 <param name="tide_output_folder" type="text" value="crux-output"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1380 label="TIDE: Output Folder" help="Tide output folder (relative to the Tide working folder). Not to be changed if the .par file will be used by SearchGUI in Galaxy"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1381 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1382 <option value="0" >0</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1383 <option value="10" >10</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1384 <option value="20" >20</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1385 <option value="30" selected="True">30</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1386 <option value="40" >40</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1387 <option value="50" >50</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1388 <option value="60" >60</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1389 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1390 <param name="tide_progress_indicator" type="integer" value="1000"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1391 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1392 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1393 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1394 <param name="tide_store_spectra" type="text" value=""
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1395 label="TIDE: Store spectra" help="Tide file name in with to store the binary spectra. Not to be changed if the .par file will be used by SearchGUI in Galaxy"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1396 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1397 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1398
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1399 <!-- Andromeda ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1400 <!-- Windows only
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1401 <conditional name="andromeda">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1402 <param name="andromeda_advanced" type="select" label="Andromeda Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1403 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1404 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1405 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1406 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1407 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1408 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1409 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1410 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1411 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1412 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1413 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1414 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1415 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1416 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1417 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1418 <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1419 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1420 <option value="CID" selected="true">CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1421 <option value="HCD">HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1422 <option value="EDT">EDT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1423 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1424 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1425 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1426 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1427 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1428 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1429 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1430 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1431 -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1432
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1433 <!-- DIRECTAG ADVANDED PARAMETERS-->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1434 <conditional name="directtag">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1435 <param name="directtag_advanced" type="select" label="DirectTag Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1436 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1437 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1438 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1439 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1440 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1441 <param name="directag_tag_length" type="integer" value="4" label="DirecTag tag length"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1442 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1443 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1444 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1445 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1446 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1447 <option value="0" selected="true">no deisotoping</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1448 <option value="1">precursor only</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1449 <option value="2">precursor and candidate</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1450 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1451 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1452 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1453 <param name="directag_max_peak_count" type="integer" value="100" label="DirecTag max peak count"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1454 <param name="directag_max_tag_count" type="integer" value="10" label="DirecTag maximum tag count"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1455 <param name="directag_tic_cutoff" type="integer" value="100" label="DirecTag TIC cutoff in percent">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1456 <validator type="in_range" min="0" max="100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1457 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1458 <param name="directag_complement_tolerance" type="float" value="0.1" label="DirecTag complement mz tolerance"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1459 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1460 <param name="directag_min_adjustment" type="float" value="-0.5" label="DirecTag minimum precursor adjustment"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1461 <param name="directag_max_adjustment" type="float" value="1.5" label="DirecTag maximum precursor adjustment"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1462 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1463 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1464 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1465 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1466 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag use charge state from M spectrum"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1467 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1468 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1469
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1470
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1471 <!-- METAMORPHEUS ADVANDED PARAMETERS-->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1472 <conditional name="metamorpheus">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1473 <param name="metamorpheus_advanced" type="select" label="MetaMorpheus Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1474 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1475 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1476 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1477 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1478 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1479 <conditional name="metamorpheus_search">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1480 <param name="metamorpheus_search_selector" type="select" label="MetaMorpheus: Search related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1481 <option value="yes" selected="True">Set Search parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1482 <option value="no">Keep Default Search parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1483 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1484 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1485 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1486 <param name="meta_morpheus_search_type" type="select" label="MetaMorpheus search type">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1487 <option value="Classic" selected="true">Classic</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1488 <option value="Modern">Modern</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1489 <option value="NonSpecific">NonSpecific</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1490 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1491 <param name="meta_morpheus_num_partitions" type="integer" value="1" label="MetaMorpheus number of partitions when indexing"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1492 <param name="meta_morpheus_dissociation_type" type="select" label="MetaMorpheus dissociation type">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1493 <option value="HCD" selected="true">HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1494 <option value="CID">CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1495 <option value="ECD">ECD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1496 <option value="ETD">ETD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1497 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1498 <param name="meta_morpheus_max_mods_for_peptide" type="integer" value="2" label="MetaMorpheus maximum modifications per peptide"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1499 <param name="meta_morpheus_meth" type="select" label="MetaMorpheus initiator methionine behavior">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1500 <option value="Undefined" >Undefined</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1501 <option value="Retain">Retain</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1502 <option value="Cleave">Cleave</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1503 <option value="Variable" selected="true">Variable</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1504 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1505 <param name="meta_morpheus_score_cutoff" type="float" value="5.0" label="MetaMorpheus score cutoff"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1506 <param name="meta_morpheus_use_delta_score" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus use delta score"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1507 <param name="meta_morpheus_mass_diff_acceptor_type" type="select" label="MetaMorpheus mass difference acceptor type">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1508 <option value="Exact">Exact</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1509 <option value="OneMM" selected="true">OneMM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1510 <option value="TwoMM">TwoMM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1511 <option value="ThreeMM" >ThreeMM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1512 <option value="PlusOrMinusThreeMM">PlusOrMinusThreeMM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1513 <option value="ModOpen">ModOpen</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1514 <option value="Open">Open</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1515 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1516 <param name="meta_morpheus_min_pep_length" type="integer" value="8"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1517 label="MetaMorpheus minimum peptide length" help="Minimum length for a peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1518 <param name="meta_morpheus_max_pep_length" type="integer" value="30"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1519 label="MetaMorpheus maximum peptide length" help="Maximum length for a peptide to be considered"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1520 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1521 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1522
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1523 <conditional name="metamorpheus_output">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1524 <param name="metamorpheus_output_selector" type="select" label="MetaMorpheus: Output related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1525 <option value="yes" >Set Output parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1526 <option value="no" selected="True">Keep Default Output parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1527 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1528 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1529 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1530 <param name="meta_morpheus_write_mzid" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus write mzid"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1531 <param name="meta_morpheus_write_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus write pepxml"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1532 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1533 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1534
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1535 <conditional name="metamorpheus_deisotoping">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1536 <param name="metamorpheus_deisotoping_selector" type="select" label="MetaMorpheus: Deisotoing related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1537 <option value="yes" >Set Deisotoping parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1538 <option value="no" selected="True">Keep Default Deisotoping parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1539 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1540 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1541 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1542 <param name="meta_morpheus_use_provided_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus use provided precursor info"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1543 <param name="meta_morpheus_do_prec_deconv" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus do precursor deconvolution"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1544 <param name="meta_morpheus_deconv_int_ratio" type="float" value="3.0" label="MetaMorpheus deconvolution intensity ratio"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1545 <param name="meta_morpheus_deconv_mass_tol" type="float" value="4.0" label="MetaMorpheus score cutoff"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1546 <param name="meta_morpheus_deconv_mass_tol_type" type="select" label="MetaMorpheus deoconvolution mass tolerance type">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1547 <option value="PPM" selected="true">PPM</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1548 <option value="Absolute">Absolute</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1549 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1550 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1551 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1552
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1553
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1554 <conditional name="metamorpheus_proteingrouping">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1555 <param name="metamorpheus_proteingrouping_selector" type="select" label="MetaMorpheus: Protein grouping related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1556 <option value="yes" >Set Protein grouping parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1557 <option value="no" selected="True">Keep Default Protein grouping parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1558 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1559 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1560 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1561 <param name="meta_morpheus_mod_peptides_are_different" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus modified peptides are different"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1562 <param name="meta_morpheus_no_one_hit_wonders" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus exclude one hit wonders"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1563 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1564 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1565
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1566
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1567
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1568 <conditional name="metamorpheus_peaktrimming">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1569 <param name="metamorpheus_peaktrimming_selector" type="select" label="MetaMorpheus: Peak trimming related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1570 <option value="yes" >Set Peak trimming parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1571 <option value="no" selected="True">Keep Default Peak trimming parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1572 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1573 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1574 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1575 <param name="meta_morpheus_trim_ms1" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus trim MS1 peaks"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1576 <param name="meta_morpheus_trim_msms" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus trim MSMS peaks"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1577 <param name="meta_morpheus_num_peaks_per_window" type="integer" value="200" label="MetaMorpheus number of peaks per window" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1578 <param name="meta_morpheus_min_allowed_int_ratio_to_base_peak" type="float" value="0.01" label="MetaMorpheus minimum allowed intensity ratio to base peak"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1579 <param name="meta_morpheus_window_with_thompson" type="integer" optional="true" label="MetaMorpheus window width in Thompson" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1580 <param name="meta_morpheus_num_windows" type="integer" optional="true" label="MetaMorpheus number of windows" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1581 <param name="meta_morpheus_norm_across_all_windows" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus normalize peaks across all windows"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1582 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1583 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1584
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1585 <conditional name="metamorpheus_silico">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1586 <param name="metamorpheus_silico_selector" type="select" label="MetaMorpheus: Silico digestion related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1587 <option value="yes" >Set Silico digestion parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1588 <option value="no" selected="True">Keep Default Silico digestion parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1589 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1590 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1591 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1592 <param name="meta_morpheus_frag_term" type="select" label="MetaMorpheus fragmentation terminus">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1593 <option value="Both" selected="true">Both</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1594 <option value="N">N</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1595 <option value="C">C</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1596 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1597 <param name="meta_morpheus_max_frag_size" type="float" value="30000.0" label="MetaMorpheus maximum fragmentation size"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1598 <param name="meta_morpheus_search_target" type="boolean" truevalue="1" falsevalue="0" checked="true" label="MetaMorpheus search target sequences"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1599 <param name="meta_morpheus_decoy_type" type="select" label="MetaMorpheus decoy type">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1600 <option value="None" selected="true">None</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1601 <option value="Reverse">Reverse</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1602 <option value="Slide">Slide</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1603 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1604 <param name="meta_morpheus_max_mod_isoforms" type="integer" value="1024" label="MetaMorpheus maximum modified isoforms" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1605 <param name="meta_morpheus_min_variant_depth" type="integer" value="1" label="MetaMorpheus minimum variant depth" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1606 <param name="meta_morpheus_max_hetrozygous_var" type="integer" value="4" label="MetaMorpheus maximum hetrozygous variants" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1607 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1608 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1609
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1610 <conditional name="metamorpheus_gptm">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1611 <param name="metamorpheus_gptm_selector" type="select" label="MetaMorpheus: G-PTM search related options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1612 <option value="yes" >Set G-PTM search parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1613 <option value="no" selected="True">Keep Default G-PTM search parameters</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1614 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1615 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1616 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1617 <param name="meta_morpheus_gptm" type="boolean" truevalue="1" falsevalue="0" checked="false" label="MetaMorpheus run G-PTM"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1618 <param name="meta_morpheus_gptm_categories" type="select" display="checkboxes" multiple="True"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1619 label="MetaMorpheus G-PTM categories to include in the G-PTM search">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1620 <option value="common_fixed_variable" >Common Fixed and Variable</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1621 <option value="common_biological" selected="true">Common Biological</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1622 <option value="common_artifact" selected="true">Common Artifact</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1623 <option value="metal" selected="true">Metal</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1624 <option value="less_common">Less Common</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1625 <option value="labeling">Labeling</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1626 <option value="subs_1n">Substitution (1 Nucleotide)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1627 <option value="subs_2n">Substitution (2+ Nucleotides)</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1628 <option value="other">Other</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1629 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1630 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1631 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1632
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1633
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1634 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1635 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1636
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1637
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1638 <!-- NOVOR ADVANDED PARAMETERS-->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1639 <conditional name="novor">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1640 <param name="novor_advanced" type="select" label="Novor Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1641 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1642 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1643 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1644 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1645 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1646 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1647 <option value="HCD" selected="True">HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1648 <option value="CID">CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1649 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1650 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1651 <option value="Trap" >Trap</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1652 <option value="TOF" >TOF</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1653 <option value="FT" selected="True">FT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1654 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1655 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1656 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1657
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1658 <!-- PEPNOVO+ ADVANDED PARAMETERS-->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1659 <conditional name="pepnovo">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1660 <param name="pepnovo_advanced" type="select" label="PepNovo+ Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1661 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1662 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1663 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1664 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1665 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1666 <param name="pepnovo_hitlist_length" type="integer" value="10" label="PepNovo+ number of de novo solutions [0-2000], default is '10'.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1667 <validator type="in_range" min="0" max="2000" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1668 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1669 <param name="pepnovo_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ estimate precursor charge option."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1670 <param name="pepnovo_correct_prec_mass" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ correct precursor mass option."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1671 <param name="pepnovo_discard_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="PepNovo+ discard low quality spectra option."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1672 <param name="pepnovo_generate_blast" type="boolean" truevalue="1" falsevalue="0" checked="false" label="PepNovo+ generate a BLAST query."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1673 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1674 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1675
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1676 <!-- PNOVO+ ADVANDED PARAMETERS-->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1677 <conditional name="pnovo">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1678 <param name="pnovo_advanced" type="select" label="pNovo+ Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1679 <option value="yes">Advanced</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1680 <option value="no" selected="True">Default</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1681 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1682 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1683 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1684 <param name="pnovo_num_peptides" type="integer" value="10" label="pNovo+ number of peptides per spectrum, default is '10'."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1685 <param name="pnovo_lower_prec" type="integer" value="300" label="pNovo+ minimum precursor mass, default is '300'."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1686 <param name="pnovo_upper_prec" type="integer" value="5000" label="pNovo+ maximum precursor mass, default is '5000'."/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1687 <param name="pnovo_activation" type="select" label="pNovo+ activation type (HCD, CID or EDT)">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1688 <option value="HCD" selected="True">HCD</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1689 <option value="CID" >CID</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1690 <option value="EDT">EDT</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1691 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1692 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1693 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1694 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1695
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1696
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1697
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1698
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1699
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1700
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1701
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1702
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1703
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1704
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1705 <!-- ADVANCED PARAMETERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1706
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1707 <section name="advanced_options" expanded="false" title="Show/Hide advanced options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1708
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1709 <!-- SPECTRUM ANNOTATION -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1710
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1711 <section name="spectrum_annotation_options" expanded="false" title="Spectrum Annotation Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1712 <param name="annotation_level" label="Percent of the possible annotations relative to the most intensive peak" help="The intensity percentile to consider for annotation, e.g. 0.75 means that the 25% most intense peaks will be annotated, default is 0.75." value="0.75" type="float">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1713 <validator type="in_range" min="0" max="1" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1714 </param>
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
1715 <param name="annotation_mz_tolerance" label="Fragment ion annotation accuracy" help=" The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance." value="0.5" type="float" />
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1716 <param name="annotation_high_resolution" label="High resolution" help="The most accurate peak will be selected within the m/z tolerance if chosen" truevalue="1" falsevalue="0" checked="true" type="boolean"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1717 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1718
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1719 <!-- SEQUENCE MATCHING -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1720
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1721 <section name="sequence_matching_options" expanded="false" title="Sequence Matching Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1722 <param name="sequence_matching_type" label="The peptide to protein sequence matching type" type="select">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1723 <option value="0">Character Sequence</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1724 <option value="1">Amino Acids</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1725 <option value="2" selected="true">Indistinguishable Amino Acids</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1726 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1727 <param name="sequence_matching_x" label="The maximal share of Xs in a sequence" help="0.25 means 25% of Xs" value="0.25" type="float">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1728 <validator type="in_range" min="0" max="1" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1729 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1730 <param name="sequence_matching_enzymatic_tags" label="Tags should only be mapped to enzymatic peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1731 <param name="sequence_matching_max_ptms_per_tag" label="The maximum number of PTMs per peptide when mapping tags" type="integer" value="3">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1732 <validator type="in_range" min="0" max="2147483647" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1733 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1734 <param name="sequence_matching_min_amino_acid_score" label="The minimum amino acid score when mapping tags" type="integer" value="30">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1735 <validator type="in_range" min="0" max="2147483647" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1736 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1737 <param name="sequence_matching_min_tag_length" label="The minimum tag length when mapping tags" type="integer" value="3">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1738 <validator type="in_range" min="0" max="2147483647" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1739 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1740
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1741 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1742
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1743
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1744 <!-- IMPORT FILTERS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1745
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1746 <section name="import_filters_options" expanded="false" title="Import filters">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1747 <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="8" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1748 <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1749 <param name="max_precursor_error" type="float" label="Maximum Precursor Error" help="The higher precursor mass error allowed in order to filter out outliers" value="10" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1750 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select" >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1751 <option value="1">ppm</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1752 <option value="0">Daltons</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1753 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1754 <param name="missed_cleavages_min" type="integer" label="Minimal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1755 <param name="missed_cleavages_max" type="integer" label="Maximal number of missed cleavages to consider when importing identification files" help="Default is no filter" value="" optional="true"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1756 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" help="If true, peptides presenting unrecognized PTMs will be excluded" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1757 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1758
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1759
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1760 <!-- PTM LOCALIZATION -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1761
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1762 <section name="ptm_localization_options" expanded="false" title="PTM Localizacion">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1763 <conditional name="ptm_score">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1764 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1765 <option value="1" selected="True">PhosphoRS</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1766 <option value="2">None</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1767 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1768 <when value="1">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1769 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1770 <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="95.0" type="float"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1771 help="Automatic mode will be used if not set" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1772 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1773 <when value="2" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1774 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1775 <param name="ptm_sequence_matching_type" type="select" label="The modification to peptide sequence matching type." >
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1776 <option value="0">Character Sequence</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1777 <option value="1" selected="true">Amino Acids</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1778 <option value="2">Indistinguishable Amino Acids</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1779 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1780 <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1781 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1782
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1783
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1784 <!-- GENE ANNOTATION -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1785
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1786 <section name="gene_annotation_options" expanded="false" title="Gene Annotation">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1787 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1788 label="gene mappings will be used and saved along with the project (UniProt databases only)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1789 help="This should only be enabled for UniProt databaases" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1790 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1791 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1792 help="This should only be enabled for UniProt databaases" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1793 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1794
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1795
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1796 <!-- PROTEIN INFERENCE -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1797
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1798 <section name="protein_inference_options" expanded="false" title="Protein Inference">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1799 <conditional name="simplify_protein_groups_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1800 <param name="simplify_protein_groups_selector" type="select" label="Simplify protein groups">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1801 <option value="yes" selected="True">Yes</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1802 <option value="no">No</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1803 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1804 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1805 <when value="yes">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1806 <param name="simplify_protein_groups_evidence" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1807 label="Based on Uniprot evidence level"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1808 <param name="simplify_protein_groups_confidence" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1809 label="Based on the peptide confidence"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1810 <param name="simplify_protein_groups_confidence_threshold" value="0.05" type="float"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1811 label="Confidence below which a peptide is ignored"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1812 <param name="simplify_protein_groups_enzymaticity" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1813 label="Based on Enzymaticity"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1814 <param name="simplify_protein_groups_variant" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1815 label="Based on Variant Mapping"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1816 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1817 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1818 <param name="simplify_protein_pi_modifications" type="boolean" truevalue="1" falsevalue="0" checked="true"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1819 label="Account for modifications when mapping peptides to proteins"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1820 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1821
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1822 <!-- VALIDATION LEVELS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1823
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1824 <section name="validation_levels_options" expanded="false" title="Validation Levels">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1825 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1826 <validator type="in_range" min="0" max="100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1827 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1828 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1829 <validator type="in_range" min="0" max="100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1830 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1831 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1832 <validator type="in_range" min="0" max="100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1833 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1834 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1835
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1836
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1837 <!-- FRACTION ANALYSIS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1838
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1839 <section name="fraction_analysis_options" expanded="false" title="Fraction Analysis">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1840 <param name="protein_fraction_mw_confidence" value="95.0" type="float"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1841 label="Minimum confidence required for a protein in the fraction MW plot (in percentage)"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1842 help="default 95%: '95.0'">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1843 <validator type="in_range" min="0" max="100" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1844 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1845 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1846
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1847
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1848 <!-- DATABASE PROCESSING OPTIONS -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1849
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1850 <section name="database_processing_options" expanded="false" title="Database Processing Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1851 <conditional name="decoy_conditional">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1852 <param name="create_decoy_selector" type="select"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1853 label="Create a concatenated target/decoy database before running PeptideShaker"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1854 help="Selecting this option will help PeptideShaker calculate FDR values">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1855 <option value="yes" selected="True">Yes</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1856 <option value="no" >No</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1857 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1858 <when value="no" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1859 <when value="yes">
61
3ec27b4cee7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
galaxyp
parents: 59
diff changeset
1860 <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag">
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1861 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1862 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1863 <option value="0">Prefix</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1864 <option value="1" selected="True">Suffix</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1865 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1866 </when>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1867 </conditional>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1868 <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix.">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1869 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1870 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1871
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1872 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1873
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1874 </inputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1875 <outputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1876 <data name="Identification_Parameters_File" format="json" from_work_dir="IdentificationParametersOutput.par" label="${tool.name}: PAR file" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1877 </outputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1878 <tests>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1879
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1880 <!-- Test that default parameters generates a standard par file -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1881 <test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1882 <param name="xtandem_advanced" value="yes"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1883 <param name="xtandem_refine_selector" value="no"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1884 <output name="Identification_Parameters_File" file="Identification_Parameters_default.par" ftype="json" compare="sim_size" delta="1000" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1885 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1886 <!-- Test specific parameters with modifications -->
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1887 <test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1888 <param name="precursor_ion_tol" value="100"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1889 <param name="fixed_modifications" value="Carbamidomethylation of C"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1890 <param name="variable_modifications" value="Oxidation of M"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1891 <param name="min_charge" value="1"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1892 <param name="max_charge" value="3"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1893 <param name="xtandem_advanced" value="yes"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1894 <param name="xtandem_refine_selector" value="yes"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1895 <output name="Identification_Parameters_File" file="Identification_Parameters_specific.par" ftype="json" compare="sim_size" delta="1000" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1896 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1897
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1898 </tests>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1899 <help>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1900 **What it does**
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1901
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1902 Creates a parameters file (.par) which can be used independently by SearchGUI or PeptideShaker apps.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1903
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1904 A FASTA file with decoy sequences generated by FastaCLI is recommended if SearchGUI and PeptideShaker are going to use the output of this tool.
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1905
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1906 </help>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1907 <expand macro="citations" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1908 </tool>