Mercurial > repos > galaxyp > peptideshaker

annotate searchgui.xml @ 52:864bd76db767 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
author galaxyp
date Wed, 16 Jan 2019 08:18:39 -0500
parents 58a3e6cb2598
children bb0130ff73ce
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52
864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
galaxyp
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
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2 <description>
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3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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10 <requirement type="package" version="3.0">zip</requirement>
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11 </requirements>
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12 <expand macro="stdio" />
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13 <command use_shared_home="false">
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14 <![CDATA[
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15 #from datetime import datetime
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16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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18 #set $temp_stderr = "searchgui_stderr"
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19 #set $bin_dir = "bin"
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21 mkdir output;
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22 mkdir output_reports;
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23 cwd=`pwd`;
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24 export HOME=\$cwd;
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25
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26 echo "" > $temp_stderr &&
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27
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28 ## echo the search engines to run (single quotes important because X!Tandem)
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29 echo '$search_engines_options.engines';
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30 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
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32 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
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33 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
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34
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35 #for $mgf in $peak_lists:
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36 #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
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37 ln -s -f '${mgf}' '${input_name}';
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38 #set $encoded_id = $__app__.security.encode_id($mgf.id)
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39 echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})';
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40 #end for
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41 ##ln -s "${input_database}" input_database.fasta;
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42 cp "${input_database}" input_database.fasta;
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44 ###########################################
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45 #### Set paths ####
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46 ###########################################
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47 echo 'Setting paths' &&
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48 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
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49 --exec_dir="\$cwd/${bin_dir}"
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50 -temp_folder \$cwd
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51 -log \$cwd/searchgui.log 2>> $temp_stderr &&
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53 ###########################################
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54 #### Creating decoy database ####
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55 ###########################################
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56 #if $protein_database_options.create_decoy:
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57 echo 'Creating decoy database.' &&
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58 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
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59 --exec_dir="\$cwd/${bin_dir}"
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60 -in input_database.fasta
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61 -decoy 2>> $temp_stderr &&
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62 rm input_database.fasta &&
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63 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
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64 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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65 #end if
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67 #####################################################
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68 ## generate IdentificationParameters for SearchGUI ##
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69 #####################################################
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70 echo 'setting identification parameters' &&
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71 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI
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72 --exec_dir="\$cwd/${bin_dir}"
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73 -out SEARCHGUI_IdentificationParameters.par
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75 @GENERAL_PARAMETERS@
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77 -db input_database.fasta
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78 $protein_database_options.use_gene_mapping
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79 #if $protein_database_options.use_gene_mapping:
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80 $protein_database_options.update_gene_mapping
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81 #else:
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82 -updateGeneMapping 0
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83 #end if
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84
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85 #if $advanced_options.xtandem.xtandem_advanced == "yes"
21
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iracooke
parents: 20
diff changeset
86
33
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galaxyp
parents: 32
diff changeset
87 -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
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galaxyp
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diff changeset
88 -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
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galaxyp
parents: 32
diff changeset
89 -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
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galaxyp
parents: 32
diff changeset
90 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
91 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
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galaxyp
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diff changeset
92 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
43
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galaxyp
parents: 42
diff changeset
93 -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
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galaxyp
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diff changeset
94 -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
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galaxyp
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diff changeset
95 -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
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galaxyp
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diff changeset
96 -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
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galaxyp
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diff changeset
97 -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
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galaxyp
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diff changeset
98 -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
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galaxyp
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diff changeset
99 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
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galaxyp
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diff changeset
100 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
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iracooke
parents: 20
diff changeset
101
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galaxyp
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diff changeset
102 #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
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iracooke
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diff changeset
103 -xtandem_refine 1
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galaxyp
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diff changeset
104 -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
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galaxyp
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105 -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
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galaxyp
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106 -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
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galaxyp
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107 -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
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galaxyp
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108 -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
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galaxyp
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109 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
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galaxyp
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110 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
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galaxyp
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diff changeset
111
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iracooke
parents: 20
diff changeset
112 #end if
43
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galaxyp
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diff changeset
113 #else
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galaxyp
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114 -xtandem_output_spectra 1
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iracooke
parents: 20
diff changeset
115 #end if
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iracooke
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diff changeset
116
33
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117 #if $advanced_options.omssa.omssa_advanced == "yes"
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galaxyp
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118 -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
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galaxyp
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119 -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
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galaxyp
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120 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
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galaxyp
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121 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
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galaxyp
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122 -omssa_memory ${advanced_options.omssa.omssa_memory}
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galaxyp
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123 -omssa_neutron ${advanced_options.omssa.omssa_neutron}
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galaxyp
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124 -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
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galaxyp
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125 -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
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galaxyp
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126 -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
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galaxyp
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127 -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
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galaxyp
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128 -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
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galaxyp
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129 -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
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galaxyp
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130 -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
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galaxyp
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131 -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
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galaxyp
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132 -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
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galaxyp
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133 -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
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galaxyp
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134 -omssa_methionine ${advanced_options.omssa.omssa_methionine}
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galaxyp
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135 -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
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galaxyp
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136 -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
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galaxyp
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137 -omssa_fraction ${advanced_options.omssa.omssa_fraction}
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galaxyp
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138 -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
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galaxyp
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139 -omssa_charge ${advanced_options.omssa.omssa_charge}
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galaxyp
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140 -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
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galaxyp
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141 -omssa_forward ${advanced_options.omssa.omssa_forward}
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galaxyp
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142 -omssa_rewind ${advanced_options.omssa.omssa_rewind}
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galaxyp
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143 -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
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galaxyp
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144 -omssa_corr ${advanced_options.omssa.omssa_corr}
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galaxyp
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145 -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
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galaxyp
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146 -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
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galaxyp
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147 -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
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galaxyp
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148 -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
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149 -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
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150 -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
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galaxyp
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151 -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
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galaxyp
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152 -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
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153 -omssa_format ${advanced_options.omssa.omssa_format}
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iracooke
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154 #end if
20
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iracooke
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155
33
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156 #if $advanced_options.msgf.msgf_advanced == "yes"
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157 -msgf_decoy ${advanced_options.msgf.msgf_decoy}
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galaxyp
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158 -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
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galaxyp
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159 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
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160 -msgf_termini ${advanced_options.msgf.msgf_termini}
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161 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
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162 -msgf_instrument ${advanced_options.msgf.msgf_instrument}
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163 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
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164 -msgf_protocol ${advanced_options.msgf.msgf_protocol}
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165 -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
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166 -msgf_additional ${advanced_options.msgf.msgf_additional}
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167 #end if
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168
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169 #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
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170 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
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171 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
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172 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
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173 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
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174 #end if
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175
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176 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
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177 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
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178 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
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179 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
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180 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
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181 -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
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182 -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
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183 -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
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184 -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
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185 -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
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186 -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
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187 -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
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188 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
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189 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
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190 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
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191 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
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192 #end if
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193
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194
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195 #* Not working in tests
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196 #if $advanced_options.andromeda.andromeda_advanced == "yes"
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197 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
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198 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
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199 -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
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200 -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
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201 -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
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202 -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
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203 -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
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204 -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
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205 -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
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206 -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
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207 -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
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208 -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
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209 -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
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210 -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
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211 -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
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212 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
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213 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
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214 #end if
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215 *#
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216
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217 #if $advanced_options.tide.tide_advanced == "yes"
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218 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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219 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
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220 #end if
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221 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
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222 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
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223 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
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224 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
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225 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
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226 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
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227 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
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228 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
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229 -tide_verbosity ${advanced_options.tide.tide_verbosity}
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230 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
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231 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
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232 -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
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233 -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
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234 -tide_max_psms ${advanced_options.tide.tide_max_psms}
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235 -tide_compute_p ${advanced_options.tide.tide_compute_p}
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236 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
44
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237 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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238 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
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239 #end if
33
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240 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
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241 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
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242 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
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243 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
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244 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
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245 -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
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246 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
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247 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
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248 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
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249 -tide_concat ${advanced_options.tide.tide_concat}
44
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250
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251 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
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252 #for $format in $formats:
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253 #if str($advanced_options.tide.tide_export).strip() == $format:
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254 -$format 1
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255 #else:
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256 -$format 0
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257 #end if
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258
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259 #end for
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260
33
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261 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
44
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262
21
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263 #end if
44
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264
21
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265
33
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266 #if $advanced_options.comet.comet_advanced == "yes"
21
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267
33
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268 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
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269 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
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270 -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
30
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271
33
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272 -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
21
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273
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274
33
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275 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
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276 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
21
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277 #end if
43
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278
33
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279 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
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280 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
21
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281 #end if
43
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282
33
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283 -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
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284 -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
20
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285 #end if
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286
33
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287 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
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288 -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
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289 -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
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290 -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
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291 -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
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292 -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
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293 -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
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294 -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
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295 -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
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296 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
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297 #end if
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298
33
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299 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
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300 -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
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301 -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
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302 #end if
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303 #end if
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304
33
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305 #if $advanced_options.directtag.directtag_advanced == "yes"
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306 -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
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307 -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
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308 -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
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309 -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
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310 -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
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311 -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
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312 -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
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313 -directag_charge_states ${advanced_options.directtag.directag_charge_states}
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314 #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
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315 -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
30
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316 #end if
33
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317 -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
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318 -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
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galaxyp
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diff changeset
319 -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
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galaxyp
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320 -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
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galaxyp
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321 -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
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galaxyp
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322 -directag_tag_length ${advanced_options.directtag.directag_tag_length}
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galaxyp
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323 -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
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galaxyp
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324 -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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325 -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
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galaxyp
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326 -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
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galaxyp
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327 -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
30
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328 #end if
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galaxyp
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329
33
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330 #if $advanced_options.novor.novor_advanced == "yes"
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galaxyp
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331 -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
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galaxyp
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332 -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
30
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333 #end if
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334
20
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iracooke
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335 2> $temp_stderr)
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336 &&
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337
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338 ################
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339 ## Search CLI ##
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iracooke
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340 ################
47
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341 echo 'running search gui' &&
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342 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
30
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343 --exec_dir="\$cwd/${bin_dir}"
20
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344 -spectrum_files \$cwd
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345 -output_folder \$cwd/output
24
815f93bb3e1b Uploaded
galaxyp
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346 -id_params SEARCHGUI_IdentificationParameters.par
20
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347
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348 -threads "\${GALAXY_SLOTS:-12}"
21
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349
33
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galaxyp
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350 #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
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galaxyp
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351 -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
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galaxyp
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352 $advanced_options.searchgui_advanced.missing_titles
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galaxyp
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353 -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
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galaxyp
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354 -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}"
21
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iracooke
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355 #end if
20
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iracooke
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356
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iracooke
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357 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
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358 ## the tree is generated afterwards in PeptideShaker
26
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359 ## -protein_index 0
20
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360
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361 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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362
33
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363 #set $engines_list = str($search_engines_options.engines).split(',')
21
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iracooke
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364 #if 'X!Tandem' in $engines_list:
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iracooke
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365 -xtandem 1
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iracooke
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366 #else
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iracooke
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367 -xtandem 0
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iracooke
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368 #end if
20
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369
21
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370 #if 'MyriMatch' in $engines_list:
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iracooke
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371 -myrimatch 1
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iracooke
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372 #else
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iracooke
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373 -myrimatch 0
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iracooke
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374 #end if
20
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375
21
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376 #if 'MSGF' in $engines_list:
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iracooke
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377 -msgf 1
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iracooke
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378 #else
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iracooke
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379 -msgf 0
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iracooke
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380 #end if
20
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381
21
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382 #if 'OMSSA' in $engines_list:
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iracooke
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383 -omssa 1
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iracooke
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384 #else
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iracooke
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385 -omssa 0
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iracooke
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386 #end if
20
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387
21
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388 #if 'Comet' in $engines_list:
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iracooke
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389 -comet 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
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diff changeset
390 #else
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iracooke
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391 -comet 0
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iracooke
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392 #end if
20
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393
21
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iracooke
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394 #if 'Tide' in $engines_list:
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iracooke
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395 -tide 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
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396 #else
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iracooke
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397 -tide 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
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398 #end if
20
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iracooke
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399
21
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iracooke
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400 #if 'MS_Amanda' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
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diff changeset
401 -ms_amanda 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
402 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
403 -ms_amanda 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
404 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
405
24
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
406 #if 'Andromeda' in $engines_list:
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
407 -andromeda 1
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
408 #else
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
409 -andromeda 0
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
410 #end if
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
411
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
412 #if 'Novor' in $engines_list:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
413 -novor 1
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
414 #else
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
415 -novor 0
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
416 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
417
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
418 #if 'DirecTag' in $engines_list:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
419 -directag 1
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
420 #else
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
421 -directag 0
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
422 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
423
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
424 ## single zip file
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
425 -output_option 0
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
426
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
427 ## mgf and database in output
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
428 -output_data 1
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
429
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
430 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
431
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
432 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
433
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
434 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
435
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
436 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
437
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 24
diff changeset
438 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
24
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
439
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
440 cat $temp_stderr 2>&1;
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
441 ]]>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
442 </command>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
443 <inputs>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
444
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
445 <param format="fasta" name="input_database" type="data" label="Protein Database"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
446 help="Select FASTA database from history"/>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
447 <section name="protein_database_options" expanded="false" title="Protein Database Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
448 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
449 label="Create a concatenated target/decoy database before running PeptideShaker"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
450 help="Selecting this option will help PeptideShaker calculate FDR values" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
451 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
452 label="gene mappings will be used and saved along with the project (UniProt databases only)"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
453 help="This should only be enabled for UniProt databaases" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
454 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
455 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
26
3ef5a7dd1a36 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
parents: 24
diff changeset
456 help="This should only be enabled for UniProt databaases" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
457 </section>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
458 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
459 help="Select appropriate MGF dataset(s) from history" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
460
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
461 <!-- Search Engine Selection -->
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
462 <section name="search_engines_options" expanded="true" title="Search Engine Options">
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
463 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
464 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
465 <option value="X!Tandem" selected="True">X!Tandem</option>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
466
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
467 <option value="MSGF" selected="True">MS-GF+</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
468 <option value="OMSSA" selected="True">OMSSA</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
469 <option value="Comet">Comet</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
470 <option value="Tide">Tide</option>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
471 <option value="MyriMatch">MyriMatch</option>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
472 <option value="MS_Amanda">MS_Amanda</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
473 <!-- Windows only
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
474 <option value="Andromeda">Andromeda</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
475 -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
476 <!-- New with version 3.0
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
477 -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
478 <!--working in tests
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
479 -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
480 <option value="DirecTag">DirecTag</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
481 <option value="Novor">Novor (Select for non-commercial use only)</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
482 <validator type="no_options" message="Please select at least one output file" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
483 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
484 </section>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
485
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
486
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
487 <!-- General Parameters -->
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
488 <expand macro="general_options"/>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
489
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
490
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
491 <section name="advanced_options" expanded="false" title="Andvanced Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
492 <!-- Optional Advanced SearchGUI Parameters -->
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galaxyp
parents: 32
diff changeset
493 <conditional name="searchgui_advanced">
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galaxyp
parents: 32
diff changeset
494 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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galaxyp
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495 <option value="basic" selected="True">Default</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
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496 <option value="advanced">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
497 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
498 <when value="basic" />
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galaxyp
parents: 32
diff changeset
499 <when value="advanced">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
500 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
501 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
502 <option value="0">no correction</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
503 <option value="1" selected="True">rename spectra</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
504 <option value="2">delete spectra</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
505 </param>
43
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galaxyp
parents: 42
diff changeset
506
33
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galaxyp
parents: 32
diff changeset
507 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
508 label="Add missing spectrum titles" help="(-missing_titles)"/>
43
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galaxyp
parents: 42
diff changeset
509
33
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galaxyp
parents: 32
diff changeset
510 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
511 help="Choose a smaller value if you are running on a machine with limited memory"/>
43
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galaxyp
parents: 42
diff changeset
512
33
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galaxyp
parents: 32
diff changeset
513 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
514 help="Choose a smaller value if you are running on a machine with limited memory"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
515 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
516 </conditional>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
517
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
518 <!-- X!TANDEM ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
519 <conditional name="xtandem">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
520 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
521 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
522 <option value="no" selected="True">Default</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
523 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
524 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
525 <when value="yes">
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
526 <param name="xtandem_npeaks" type="integer" value="50"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
527 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
528 <param name="xtandem_min_peaks" type="integer" value="15"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
529 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
530 <param name="xtandem_min_frag_mz" type="integer" value="200"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
531 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
532 <param name="xtandem_min_prec_mass" type="integer" value="200"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
533 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
534 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
535 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
536 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
537 label="X!Tandem: Dynamic Range" value="100" type="integer" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
538 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
539 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
540 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
43
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galaxyp
parents: 42
diff changeset
541 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
542 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
543 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
544 <param name="xtandem_evalue" help="Highest value for recorded peptides"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
545 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
546 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
547 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
548 <param name="xtandem_output_sequences" help="Controls output of sequence information"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
549 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
550 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
551 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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parents: 40
diff changeset
552 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
553
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
554 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
555 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
556 <option value="no" selected="True">Don't refine</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
557 <option value="yes" >Use refinement</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
558 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
559 <when value="no"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
560 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
561 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
562 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
563 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
564 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
565 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
566 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
567 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
568 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
569 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
570 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
571 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
572 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
573 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
574 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
575 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
576 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
577 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
578 </conditional>
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galaxyp
parents: 42
diff changeset
579
33
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galaxyp
parents: 32
diff changeset
580 <!-- OMSSA ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
581 <conditional name="omssa">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
582 <param name="omssa_advanced" type="select" label="OMSSA Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
583 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
584 <option value="no" selected="True">Default</option>
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iracooke
parents: 20
diff changeset
585 </param>
33
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galaxyp
parents: 32
diff changeset
586 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
587 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
588 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
589 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
590 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
591 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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galaxyp
parents: 42
diff changeset
592
33
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galaxyp
parents: 32
diff changeset
593 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
594 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
43
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galaxyp
parents: 42
diff changeset
595 <param name="omssa_neutron" type="float" value="1446.94"
33
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galaxyp
parents: 32
diff changeset
596 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
43
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galaxyp
parents: 42
diff changeset
597 <param name="omssa_low_intensity" type="float" value="0.0"
33
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galaxyp
parents: 32
diff changeset
598 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
599 <param name="omssa_high_intensity" type="float" value="0.2"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
600 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
43
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galaxyp
parents: 42
diff changeset
601 <param name="omssa_intensity_incr" type="float" value="0.0005"
33
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galaxyp
parents: 32
diff changeset
602 label="OMSSA: Intensity Increment" help="Intensity increment" />
43
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galaxyp
parents: 42
diff changeset
603 <param name="omssa_single_window_wd" type="integer" value="27"
33
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galaxyp
parents: 32
diff changeset
604 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
43
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galaxyp
parents: 42
diff changeset
605 <param name="omssa_double_window_wd" type="integer" value="14"
33
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galaxyp
parents: 32
diff changeset
606 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
43
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galaxyp
parents: 42
diff changeset
607 <param name="omssa_single_window_pk" type="integer" value="2"
33
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galaxyp
parents: 32
diff changeset
608 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
43
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galaxyp
parents: 42
diff changeset
609 <param name="omssa_double_window_pk" type="integer" value="2"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
610 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
43
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galaxyp
parents: 42
diff changeset
611 <param name="omssa_min_ann_int_pks" type="integer" value="6"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
612 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
43
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galaxyp
parents: 42
diff changeset
613 <param name="omssa_min_annotated_peaks" type="integer" value="2"
33
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galaxyp
parents: 32
diff changeset
614 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
43
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galaxyp
parents: 42
diff changeset
615 <param name="omssa_min_peaks" type="integer" value="4"
33
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galaxyp
parents: 32
diff changeset
616 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
617 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
618 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
43
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galaxyp
parents: 42
diff changeset
619 <param name="omssa_max_ladders" type="integer" value="128"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
620 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
621 <param name="omssa_max_frag_charge" type="integer" value="2"
33
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galaxyp
parents: 32
diff changeset
622 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
43
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galaxyp
parents: 42
diff changeset
623 <param name="omssa_fraction" type="float" value="0.95"
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galaxyp
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diff changeset
624 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
43
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galaxyp
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diff changeset
625 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
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galaxyp
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diff changeset
626 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
43
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galaxyp
parents: 42
diff changeset
627 <param name="omssa_charge" type="select"
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galaxyp
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diff changeset
628 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
629 <option value="0" >Minus</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
630 <option value="1" selected="True">Plus</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
631 </param>
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galaxyp
parents: 42
diff changeset
632 <param name="omssa_prec_per_spectrum" type="integer" value="1"
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galaxyp
parents: 32
diff changeset
633 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
43
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galaxyp
parents: 42
diff changeset
634 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
33
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galaxyp
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diff changeset
635 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
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galaxyp
parents: 42
diff changeset
636 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
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galaxyp
parents: 32
diff changeset
637 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
43
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galaxyp
parents: 42
diff changeset
638 <param name="omssa_max_frag_series" type="integer" value="100"
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galaxyp
parents: 32
diff changeset
639 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
640 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
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galaxyp
parents: 32
diff changeset
641 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
43
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galaxyp
parents: 42
diff changeset
642 <param name="omssa_consecutive_p" type="float" value="0.5"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
643 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
644 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
33
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galaxyp
parents: 32
diff changeset
645 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
43
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galaxyp
parents: 42
diff changeset
646 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
647 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
648 <param name="omssa_it_replace_evalue" type="float" value="0.01"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
649 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
650 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
651 label="OMSSA: Remove Precursor" help="Remove precursors" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
652 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
653 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
654 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
655 label="OMSSA: Remove Precursor" help="Remove precursors" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
656 <param name="omssa_max_evalue" type="float" value="100"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
657 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
658 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
659 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
660 <param name="omssa_it_replace_evalue" type="float" value="100"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
661 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
662 <param name="omssa_hitlist_length" type="integer" value="0"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
663 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
664 <param name="omssa_hitlist_charge" type="integer" value="30"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
665 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
666 <param name="omssa_min_pep_length" type="integer" value="4"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
667 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
668 <param name="omssa_max_pep_length" type="integer" value="40"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
669 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
670 <param name="omssa_format" label="OMSSA output format" type="select" >
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
671 <option value="0" selected="True">OMX</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
672 <option value="1" >CSV</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
673 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
674 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
675 </conditional>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
676
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
677 <!-- MS-GF+ ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
678 <conditional name="msgf">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
679 <param name="msgf_advanced" type="select" label="MSGF Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
680 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
681 <option value="no" selected="True">Default</option>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
682 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
683 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
684 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
685 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
686 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
687 <param name="msgf_min_pep_length" type="integer" value="6"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
688 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
689 <param name="msgf_max_pep_length" type="integer" value="30"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
690 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
691 <param name="msgf_termini" type="select" format="txt"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
692 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
693 <option value="0">0 (ie non-specific cleavage)</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
694 <option value="1">1 (ie semi-tryptic cleavage)</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
695 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
696 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
697 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
698
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
699 <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
700 <option value="0" selected="True">Low-res LCQ/LTQ</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
701 <option value="1" >High-res LTQ</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
702 <option value="2" >TOF</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
703 <option value="3" >Q-Exactive</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
704 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
705 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
706 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
707 <option value="1" >CID</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
708 <option value="2" >ETD</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
709 <option value="3" >HCD</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
710 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
711 <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
712 <option value="0" selected="True">Automatic</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
713 <option value="1" >Phosphorylation</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
714 <option value="2" >iTRAQ</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
715 <option value="3" >iTRAQPhospho</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
716 <option value="4" >TMT</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
717 <option value="5" >Standard</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
718 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
719 <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
720 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
721 <option value="0" selected="True">output basic scores only</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
722 <option value="1" >output additional features</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
723 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
724 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
725 </conditional>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
726
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
727 <!-- MS-AMANDA ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
728 <conditional name="ms_amanda">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
729 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
730 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
731 <option value="no" selected="True">Default</option>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
732 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
733 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
734 <when value="yes">
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
735 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
736 label="MS Amanda: Generate Decoys" help="generate decoys" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
737 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
738 help="MS Amanda instrument id option. Available ion types are listed here.">
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
739
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
740 <option value="b, y" selected="True">b, y</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
741 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
742 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
743 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
744 <option value="a, b, y" >a, b, y</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
745 <option value="a, b, y, Imm" >a, b, y, Imm</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
746 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
747 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
748 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
749 <option value="b, y, INT" >b, y, INT</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
750 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
751 <option value="a, b, y, INT" >a, b, y, INT</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
752 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
753 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
754 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
755 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
756
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
757 </param>
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
758 <param name="ms_amanda_max_rank" type="integer" value="10"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
759 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
760 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
761 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
762 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
763 </conditional>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
764
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
765
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
766 <!-- TIDE ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
767 <conditional name="tide">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
768 <param name="tide_advanced" type="select" label="TIDE Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
769 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
770 <option value="no" selected="True">Default</option>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
771 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
772 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
773 <when value="yes">
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
774 <param name="tide_num_ptms" type="integer" value="" optional="true"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
775 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
776 <param name="tide_num_ptms_per_type" type="integer" value="2"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
777 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
778 <param name="tide_min_pep_length" type="integer" value="6"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
779 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
780 <param name="tide_max_pep_length" type="integer" value="30"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
781 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
782 <param name="tide_min_prec_mass" type="float" value="200.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
783 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
784 <param name="tide_max_prec_mass" type="float" value="7200.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
785 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
786 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
787 <option value="none" selected="True">none</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
788 <option value="shuffle" >shuffle</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
789 <option value="peptide-revers" >peptide-reverse</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
790 <option value="protein-reverse" >protein-reverse</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
791 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
792 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
793 <option value="N" >N</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
794 <option value="C" >C</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
795 <option value="NC" selected="True">NC</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
796 <option value="non" >none</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
797 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
798 <param name="tide_decoy_seed" type="integer" value="1"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
799 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
800 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
801 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
802 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
803 <option value="0" >0</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
804 <option value="10" >10</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
805 <option value="20" >20</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
806 <option value="30" selected="True">30</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
807 <option value="40" >40</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
808 <option value="50" >50</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
809 <option value="60" >60</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
810 </param>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
811
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
812 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
813 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
814 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
815 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
816 <param name="tide_digestion_type" label="TIDE: 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">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
817 <option value="full-digest" selected="True">full-digest</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
818 <option value="partial-digest" >partial-digest</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
819 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
820 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
821 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
822 <param name="tide_max_psms" type="integer" value="10"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
823 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
824 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
825 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
826 <param name="tide_min_spectrum_mz" type="float" value="0.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
827 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
828 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
829 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
830 <param name="tide_min_spectrum_peaks" type="integer" value="20"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
831 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
832 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
833 <option value="1" >1</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
834 <option value="2" >2</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
835 <option value="3" >3</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
836 <option value="all" selected="True">all</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
837 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
838 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
839 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
840 <param name="tide_remove_prec_tol" type="float" value="1.5"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
841 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
842 <param name="tide_progress_indicator" type="integer" value="1000"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
843 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
844 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
845 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
846 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
847 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
848 <param name="tide_mz_bin_width" type="float" value="0.02"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
849 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
850 <param name="tide_mz_bin_offset" type="float" value="0.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
851 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
852 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
853 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
854
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
855 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
856 <option value="tide_export_text" selected="True">Text</option>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
857 <option value="tide_export_sqt" >SQT</option>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
858 <option value="tide_export_pepxml" >pepxml</option>
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
859 <option value="tide_export_mzid" >MzIdentML</option>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
860 <option value="tide_export_pin" >Percolator input file</option>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
861 </param>
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
862
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
863 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
864 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
865 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
866 </conditional>
44
f35bb9d0c93e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 43
diff changeset
867
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
868
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
869 <!-- MyriMatch ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
870 <conditional name="myrimatch">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
871 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
872 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
873 <option value="no" selected="True">Default</option>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
874 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
875 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
876 <when value="yes">
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
877 <param name="myrimatch_min_pep_length" type="integer" value="8"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
878 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
879 <param name="myrimatch_max_pep_length" type="integer" value="30"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
880 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
45
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galaxyp
parents: 44
diff changeset
881 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
882 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
883 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
884 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
885 <param name="myrimatch_num_matches" type="integer" value="10"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
886 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
887 <param name="myrimatch_num_ptms" type="integer" value="2"
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
888 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
889 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
890 <option value="CID" selected="True">CID</option>
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
891 <option value="HCD" >HCD</option>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
892 <option value="ETD" >ETD</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
893 </param>
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
894 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
895 <option value="0">None required</option>
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
896 <option value="1">At least one</option>
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
897 <option value="2" selected="True" >Both</option>
33
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galaxyp
parents: 32
diff changeset
898 </param>
43
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galaxyp
parents: 42
diff changeset
899 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
900 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
901 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
902 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
903 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
904 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)" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
905 <param name="myrimatch_intensity_classes" type="integer" value="3"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
906 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
907 <param name="myrimatch_class_multiplier" type="integer" value="2"
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
908 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" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
909 <param name="myrimatch_num_batches" type="integer" value="50"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
910 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
911 <param name="myrimatch_max_peak" type="integer" value="100"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
912 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
913 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
914 </conditional>
45
5fa8b409599e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 44
diff changeset
915
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
916
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
917 <!-- Andromeda ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
918 <!-- Windows only
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
919 <conditional name="andromeda">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
920 <param name="andromeda_advanced" type="select" label="Andromeda Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
921 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
922 <option value="no" selected="True">Default</option>
24
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
923 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
924 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
925 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
926 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
927 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
928 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
929 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
930 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
931 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
932 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
933 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
934 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
935 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
936 <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" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
937 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
938 <option value="CID" selected="true">CID</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
939 <option value="HCD">HCD</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
940 <option value="EDT">EDT</option>
20
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iracooke
parents:
diff changeset
941 </param>
33
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galaxyp
parents: 32
diff changeset
942 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
943 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
944 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
945 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
946 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
947 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
948 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
949 -->
43
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galaxyp
parents: 42
diff changeset
950
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
951 <!-- Comet ADVANCED PARAMETERS -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
952 <conditional name="comet">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
953 <param name="comet_advanced" type="select" label="Comet Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
954 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
955 <option value="no" selected="True">Default</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
956 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
957 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
958 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
959 <!-- Spectrum Related parameters -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
960 <conditional name="comet_spectrum">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
961 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
962 <option value="yes">Set Spectrum Parameters</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
963 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
964 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
965 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
966 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
967 <param name="comet_min_peaks" type="integer" value="10"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
968 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
969 <param name="comet_min_peak_int" type="float" value="0.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
970 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
971 <conditional name="comet_prec">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
972 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
973 <option value="0" selected="True" >off</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
974 <option value="1">on</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
975 <option value="2">as expected for ETD/ECD spectra</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
976 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
977 <when value="0" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
978 <when value="1">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
979 <param name="comet_remove_prec_tol" type="float" value="1.5"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
980 label="Comet: Remove Precursor Tolerance" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
981 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
982 <when value="2">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
983 <param name="comet_remove_prec_tol" type="float" value="1.5"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
984 label="Comet: Remove Precursor Tolerance" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
985 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
986 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
987 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
988 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" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
989 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
990 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" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
991 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
992 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
993 <!-- Search Related parameters -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
994 <conditional name="comet_search">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
995 <param name="comet_search_selector" type="select" label="Comet: Search Related">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
996 <option value="yes">Set Search Parameters</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
997 <option value="no" selected="True">Keep Default Search Parameters</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
998 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
999 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1000 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1001 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1002 <option value="1">semi-specific</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1003 <option value="2" selected="True">full-enzyme</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1004 <option value="8">unspecific N-term</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1005 <option value="9">unspecific C-term</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1006 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1007 <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">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1008 <option value="0" selected="True">off</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1009 <option value="1">-1,0,+1,+2,+3</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1010 <option value="2">-8,-4,0,+4,+8</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1011 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1012 <param name="comet_min_prec_mass" type="float" value="0.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1013 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1014 <param name="comet_max_prec_mass" type="float" value="10000.0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1015 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1016 <param name="comet_num_matches" type="integer" value="10"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1017 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1018 <param name="comet_max_frag_charge" type="integer" value="3"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1019 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
1020 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1021 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1022 <param name="comet_batch_size" type="integer" value="0"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1023 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" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1024 <param name="comet_num_ptms" type="integer" value="10"
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
1025 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1026 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1027 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1028 <!-- Fragment Ions Related parameters -->
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1029 <conditional name="comet_fragment_ions">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1030 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1031 <option value="yes">Set Fragment Ions Parameters</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1032 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1033 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1034 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1035 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1036 <param name="comet_frag_bin_offset" type="float" value="0.4"
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1037 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1038 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
1039 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
33
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galaxyp
parents: 32
diff changeset
1040 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1041 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1042 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1043 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1044 <conditional name="directtag">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1045 <param name="directtag_advanced" type="select" label="DirectTag Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1046 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1047 <option value="no" selected="True">Default</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1048 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1049 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1050 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1051 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1052 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1053 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1054 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1055 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1056 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1057 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1058 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1059 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1060 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1061 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1062 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1063 <option value="0" selected="true">no deisotoping</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1064 <option value="1">precursor only</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1065 <option value="2">precursor and candidate</option>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1066 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1067 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1068 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1069 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1070 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1071 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1072 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1073 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1074 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1075 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1076 </conditional>
43
7963340ab569 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 42
diff changeset
1077
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1078 <conditional name="novor">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1079 <param name="novor_advanced" type="select" label="Novor Options">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1080 <option value="yes">Advanced</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1081 <option value="no" selected="True">Default</option>
30
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galaxyp
parents: 28
diff changeset
1082 </param>
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1083 <when value="no" />
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1084 <when value="yes">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1085 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1086 <option value="HCD" selected="True">HCD</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1087 <option value="CID">CID</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1088 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1089 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1090 <option value="FT" selected="True">FT</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1091 <option value="Trap" >Trap</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1092 <option value="TOF" >TOF</option>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1093 </param>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1094 </when>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
1095 </conditional>
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
1096 </section>
20
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iracooke
parents:
diff changeset
1097 </inputs>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
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diff changeset
1098 <outputs>
21
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diff changeset
1099 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
20
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iracooke
parents:
diff changeset
1100 </outputs>
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iracooke
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diff changeset
1101 <tests>
21
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iracooke
parents: 20
diff changeset
1102
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
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diff changeset
1103 <!-- Test that specifying non-default search engines works -->
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1104 <test>
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iracooke
parents:
diff changeset
1105 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1107 <param name="precursor_ion_tol" value="100"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1108 <param name="min_charge" value="1"/>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1109 <param name="max_charge" value="3"/>
21
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diff changeset
1110 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
49
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parents: 48
diff changeset
1111 <param name="xtandem|xtandem_advanced" value="yes"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
galaxyp
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diff changeset
1112 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
47
44ca2967218c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
galaxyp
parents: 46
diff changeset
1113 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1114 </test>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1115 <!-- Test that search works with MSAmanda -->
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1116 <test>
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1118 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1119 <param name="precursor_ion_tol" value="100"/>
46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1120 <param name="min_charge" value="1"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1121 <param name="max_charge" value="3"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1122 <param name="engines" value="MS_Amanda"/>
47
44ca2967218c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
galaxyp
parents: 46
diff changeset
1123 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1124 </test>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1125
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1126 <!-- Test that specifying non-default search engines works using modifications -->
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1127 <test>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1128 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1129 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1130 <param name="precursor_ion_tol" value="100"/>
52
864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
galaxyp
parents: 49
diff changeset
1131 <param name="fixed_modifications" value="Carbamidomethylation of C"/>
864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
galaxyp
parents: 49
diff changeset
1132 <param name="variable_modifications" value="Oxidation of M"/>
46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1133 <param name="min_charge" value="1"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1134 <param name="max_charge" value="3"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1135 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
49
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
galaxyp
parents: 48
diff changeset
1136 <param name="xtandem|xtandem_advanced" value="yes"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
galaxyp
parents: 48
diff changeset
1137 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
galaxyp
parents: 48
diff changeset
1138 <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
46
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1139 </test>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1140 <!-- Test that search works with MSAmanda - with modifications -->
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1141 <test>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1142 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1143 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
baeced706dbc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
galaxyp
parents: 45
diff changeset
1144 <param name="precursor_ion_tol" value="100"/>
52
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galaxyp
parents: 49
diff changeset
1145 <param name="fixed_modifications" value="Carbamidomethylation of C"/>
864bd76db767 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
galaxyp
parents: 49
diff changeset
1146 <param name="variable_modifications" value="Oxidation of M"/>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1147 <param name="min_charge" value="1"/>
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1148 <param name="max_charge" value="3"/>
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1149 <param name="engines" value="MS_Amanda"/>
49
58a3e6cb2598 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
galaxyp
parents: 48
diff changeset
1150 <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1151 </test>
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1152 </tests>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1153 <help>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1154 **What it does**
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1155
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1156 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1157 Default: X! Tandem, OMSSA and MS-GF+ are executed.
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
1158 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1159
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1160 </help>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1161 <expand macro="citations" />
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
1162 </tool>