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annotate searchgui.xml @ 38:263440bb1900 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
author galaxyp
date Mon, 30 Apr 2018 04:41:10 -0400
parents 7b72e889dafd
children f63401dd6cbb
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263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
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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>
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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 $bin_dir = "bin"
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21 mkdir output;
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22 mkdir output_reports;
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23 cwd=`pwd`;
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24 export HOME=\$cwd;
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25
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26 ## echo the search engines to run
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27 echo "$search_engines_options.engines";
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28 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
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29
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30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
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31 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
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32
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33 #for $mgf in $peak_lists:
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34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
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35 ln -s -f '${mgf}' '${input_name}';
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36 #set $encoded_id = $__app__.security.encode_id($mgf.id)
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37 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
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38 #end for
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39 ##ln -s "${input_database}" input_database.fasta;
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40 cp "${input_database}" input_database.fasta;
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42 ###########################################
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43 #### Creating decoy database ####
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44 ###########################################
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45 #if $protein_database_options.create_decoy:
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46 echo "Creating decoy database.";
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47 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
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48 rm input_database.fasta &&
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49 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
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50 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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51 #end if
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53 #####################################################
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54 ## generate IdentificationParameters for SearchGUI ##
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55 #####################################################
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56 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
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57 --exec_dir="\$cwd/${bin_dir}"
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58 -out SEARCHGUI_IdentificationParameters.par
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60 @GENERAL_PARAMETERS@
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62 -db input_database.fasta
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63 $protein_database_options.use_gene_mapping
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64 #if $protein_database_options.use_gene_mapping:
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65 $protein_database_options.update_gene_mapping
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66 #else:
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67 -updateGeneMapping 0
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68 #end if
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69
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70 #if $advanced_options.xtandem.xtandem_advanced == "yes"
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72 -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
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73 -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
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74 -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
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75 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
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76 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
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77 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
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78 -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
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79 -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
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80 -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
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81 -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
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82 -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
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83 -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
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84 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
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85 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
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86
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diff changeset
87 #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
1
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iracooke
parents: 0
diff changeset
88 -xtandem_refine 1
23
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galaxyp
parents: 22
diff changeset
89 -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
90 -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
91 -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
92 -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
93 -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
94 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
95 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
36
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galaxyp
parents: 35
diff changeset
96
0
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galaxyp
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diff changeset
97 #end if
36
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galaxyp
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diff changeset
98 #else
17
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galaxyp
parents: 15
diff changeset
99 -xtandem_output_spectra 1
1
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iracooke
parents: 0
diff changeset
100 #end if
0
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galaxyp
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diff changeset
101
23
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galaxyp
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diff changeset
102 #if $advanced_options.omssa.omssa_advanced == "yes"
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galaxyp
parents: 22
diff changeset
103 -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
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galaxyp
parents: 22
diff changeset
104 -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
105 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
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galaxyp
parents: 22
diff changeset
106 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
107 -omssa_memory ${advanced_options.omssa.omssa_memory}
36
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galaxyp
parents: 35
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108 -omssa_neutron ${advanced_options.omssa.omssa_neutron}
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galaxyp
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109 -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
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110 -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
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galaxyp
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111 -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
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galaxyp
parents: 35
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112 -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
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galaxyp
parents: 35
diff changeset
113 -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
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galaxyp
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114 -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
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galaxyp
parents: 35
diff changeset
115 -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
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galaxyp
parents: 35
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116 -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
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galaxyp
parents: 35
diff changeset
117 -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
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galaxyp
parents: 35
diff changeset
118 -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
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galaxyp
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119 -omssa_methionine ${advanced_options.omssa.omssa_methionine}
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galaxyp
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120 -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
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galaxyp
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121 -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
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galaxyp
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122 -omssa_fraction ${advanced_options.omssa.omssa_fraction}
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galaxyp
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123 -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
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galaxyp
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124 -omssa_charge ${advanced_options.omssa.omssa_charge}
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galaxyp
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125 -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
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galaxyp
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126 -omssa_forward ${advanced_options.omssa.omssa_forward}
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galaxyp
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127 -omssa_rewind ${advanced_options.omssa.omssa_rewind}
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galaxyp
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128 -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
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galaxyp
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129 -omssa_corr ${advanced_options.omssa.omssa_corr}
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galaxyp
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130 -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
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galaxyp
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131 -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
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galaxyp
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132 -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
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galaxyp
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133 -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
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galaxyp
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134 -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
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galaxyp
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135 -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
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galaxyp
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136 -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
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galaxyp
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137 -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
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galaxyp
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138 -omssa_format ${advanced_options.omssa.omssa_format}
1
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iracooke
parents: 0
diff changeset
139 #end if
0
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140
23
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galaxyp
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141 #if $advanced_options.msgf.msgf_advanced == "yes"
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galaxyp
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142 -msgf_decoy ${advanced_options.msgf.msgf_decoy}
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galaxyp
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143 -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
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galaxyp
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144 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
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galaxyp
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145 -msgf_termini ${advanced_options.msgf.msgf_termini}
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galaxyp
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146 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
36
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147 -msgf_instrument ${advanced_options.msgf.msgf_instrument}
23
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galaxyp
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148 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
36
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galaxyp
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149 -msgf_protocol ${advanced_options.msgf.msgf_protocol}
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galaxyp
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150 -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
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galaxyp
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151 -msgf_additional ${advanced_options.msgf.msgf_additional}
1
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iracooke
parents: 0
diff changeset
152 #end if
36
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153
23
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galaxyp
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154 #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
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galaxyp
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155 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
36
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galaxyp
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156 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
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galaxyp
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157 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
23
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galaxyp
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158 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
3
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iracooke
parents: 2
diff changeset
159 #end if
36
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galaxyp
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160
23
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galaxyp
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diff changeset
161 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
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galaxyp
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162 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
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galaxyp
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163 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
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galaxyp
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164 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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165 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
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galaxyp
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166 -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
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galaxyp
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167 -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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168 -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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169 -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
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galaxyp
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170 -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
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galaxyp
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171 -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
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galaxyp
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172 -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
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galaxyp
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173 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
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galaxyp
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174 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
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galaxyp
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175 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
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176 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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177 #end if
38
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178
1
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179
17
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180 #* Not working in tests
23
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181 #if $advanced_options.andromeda.andromeda_advanced == "yes"
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182 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
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183 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
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184 -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
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185 -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
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186 -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
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187 -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
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188 -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
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189 -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
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190 -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
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191 -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
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192 -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
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193 -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
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194 -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
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195 -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
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196 -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
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197 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
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198 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
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199 #end if
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200 *#
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201
23
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202 #if $advanced_options.tide.tide_advanced == "yes"
37
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203 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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204 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
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205 #end if
23
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galaxyp
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206 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
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galaxyp
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207 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
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galaxyp
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208 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
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galaxyp
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209 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
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210 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
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211 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
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212 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
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213 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
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214 -tide_verbosity ${advanced_options.tide.tide_verbosity}
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215 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
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216 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
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217 -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
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218 -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
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219 -tide_max_psms ${advanced_options.tide.tide_max_psms}
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220 -tide_compute_p ${advanced_options.tide.tide_compute_p}
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221 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
37
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222 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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223 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
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224 #end if
23
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225 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
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226 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
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227 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
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228 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
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229 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
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230 -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
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galaxyp
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231 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
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232 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
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233 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
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234 -tide_concat ${advanced_options.tide.tide_concat}
37
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235
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236 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
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237 #for $format in $formats:
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238 #if str($advanced_options.tide.tide_export).strip() == $format:
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diff changeset
239 -$format 1
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parents: 36
diff changeset
240 #else:
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parents: 36
diff changeset
241 -$format 0
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galaxyp
parents: 36
diff changeset
242 #end if
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diff changeset
243
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
244 #end for
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galaxyp
parents: 36
diff changeset
245
23
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galaxyp
parents: 22
diff changeset
246 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
37
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247
1
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iracooke
parents: 0
diff changeset
248 #end if
37
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parents: 36
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249
1
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iracooke
parents: 0
diff changeset
250
23
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galaxyp
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diff changeset
251 #if $advanced_options.comet.comet_advanced == "yes"
1
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iracooke
parents: 0
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252
23
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galaxyp
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diff changeset
253 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
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254 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
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255 -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
18
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
256
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
257 -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
6
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iracooke
parents: 4
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258
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iracooke
parents: 4
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259
23
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galaxyp
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260 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
261 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
6
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iracooke
parents: 4
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262 #end if
36
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263
23
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galaxyp
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264 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
265 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
6
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iracooke
parents: 4
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266 #end if
36
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galaxyp
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267
23
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galaxyp
parents: 22
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268 -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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269 -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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270 #end if
6
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iracooke
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271
23
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galaxyp
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272 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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273 -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
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galaxyp
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diff changeset
274 -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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275 -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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276 -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
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galaxyp
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277 -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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278 -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
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galaxyp
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279 -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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280 -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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281 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
6
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iracooke
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282 #end if
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iracooke
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diff changeset
283
23
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galaxyp
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284 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
285 -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
286 -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
1
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iracooke
parents: 0
diff changeset
287 #end if
6
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iracooke
parents: 4
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288 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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289
23
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galaxyp
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diff changeset
290 #if $advanced_options.directtag.directtag_advanced == "yes"
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galaxyp
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291 -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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292 -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
293 -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
294 -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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295 -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
296 -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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297 -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
298 -directag_charge_states ${advanced_options.directtag.directag_charge_states}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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299 #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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300 -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
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ffed32e397cb Uploaded
galaxyp
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301 #end if
23
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galaxyp
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302 -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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303 -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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304 -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
305 -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
306 -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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307 -directag_tag_length ${advanced_options.directtag.directag_tag_length}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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308 -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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309 -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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310 -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
311 -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
312 -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
18
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
313 #end if
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diff changeset
314
23
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galaxyp
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diff changeset
315 #if $advanced_options.novor.novor_advanced == "yes"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
316 -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
317 -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
18
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galaxyp
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diff changeset
318 #end if
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galaxyp
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diff changeset
319
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
320 2> $temp_stderr)
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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321 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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322
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
323 ################
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
324 ## Search CLI ##
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
325 ################
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
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diff changeset
326 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
18
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327 --exec_dir="\$cwd/${bin_dir}"
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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328 -temp_folder `pwd`
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
329 -spectrum_files \$cwd
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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330 -output_folder \$cwd/output
15
3fa49ed11f3d Uploaded
galaxyp
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diff changeset
331 -id_params SEARCHGUI_IdentificationParameters.par
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
332
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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333 -threads "\${GALAXY_SLOTS:-12}"
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
334
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
335 #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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336 -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
337 $advanced_options.searchgui_advanced.missing_titles
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
338 -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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339 -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}"
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
340 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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341
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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342 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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343 ## the tree is generated afterwards in PeptideShaker
17
2f8e9d0351a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
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344 ## -protein_index 0
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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345
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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346 ##-makeblastdb_folder \$BLAST_ROOT_DIR
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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347
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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348 #set $engines_list = str($search_engines_options.engines).split(',')
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
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diff changeset
349 #if 'X!Tandem' in $engines_list:
1
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iracooke
parents: 0
diff changeset
350 -xtandem 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
351 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
352 -xtandem 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
353 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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354
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
355 #if 'MyriMatch' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
356 -myrimatch 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
357 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
358 -myrimatch 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
359 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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360
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
361 #if 'MSGF' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
362 -msgf 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
363 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
364 -msgf 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
365 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
366
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
367 #if 'OMSSA' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
368 -omssa 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
369 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
370 -omssa 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
371 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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372
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
373 #if 'Comet' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
374 -comet 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
375 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
376 -comet 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
377 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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378
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
379 #if 'Tide' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
380 -tide 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
381 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
382 -tide 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
383 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
384
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
385 #if 'MS_Amanda' in $engines_list:
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
386 -ms_amanda 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
387 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
388 -ms_amanda 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
389 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
390
15
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
391 #if 'Andromeda' in $engines_list:
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
392 -andromeda 1
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
393 #else
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
394 -andromeda 0
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
395 #end if
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
396
18
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
397 #if 'Novor' in $engines_list:
ffed32e397cb Uploaded
galaxyp
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diff changeset
398 -novor 1
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
399 #else
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
400 -novor 0
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
401 #end if
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
402
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
403 #if 'DirecTag' in $engines_list:
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
404 -directag 1
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
405 #else
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
406 -directag 0
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
407 #end if
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
408
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
409 ## single zip file
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
410 -output_option 0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
411
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
412 ## mgf and database in output
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
413 -output_data 1
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
414
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
415 2>> $temp_stderr)
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
416
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
417 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
418
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
419 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
420
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
421 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
422
17
2f8e9d0351a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 15
diff changeset
423 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
13
3ccfbb673089 Update to PS 1.1 and SG 2.1.1
iracooke
parents: 12
diff changeset
424
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
425 exit_code_for_galaxy=\$?;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
426 cat $temp_stderr 2>&1;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
427 (exit \$exit_code_for_galaxy)
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
428 ]]>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
429 </command>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
430 <inputs>
1
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iracooke
parents: 0
diff changeset
431
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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diff changeset
432 <param format="fasta" name="input_database" type="data" label="Protein Database"
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
433 help="Select FASTA database from history"/>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
434 <section name="protein_database_options" expanded="false" title="Protein Database Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
435 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
436 label="Create a concatenated target/decoy database before running PeptideShaker"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
437 help="Selecting this option will help PeptideShaker calculate FDR values" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
438 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
439 label="gene mappings will be used and saved along with the project (UniProt databases only)"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
440 help="This should only be enabled for UniProt databaases" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
441 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
442 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
17
2f8e9d0351a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
parents: 15
diff changeset
443 help="This should only be enabled for UniProt databaases" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
444 </section>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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445 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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446 help="Select appropriate MGF dataset(s) from history" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
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447
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
448 <!-- Search Engine Selection -->
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
449 <section name="search_engines_options" expanded="true" title="Search Engine Options">
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
450 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
451 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
452 <option value="X!Tandem" selected="True">X!Tandem</option>
36
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galaxyp
parents: 35
diff changeset
453
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
454 <option value="MSGF" selected="True">MS-GF+</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
455 <option value="OMSSA" selected="True">OMSSA</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
456 <option value="Comet">Comet</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
457 <option value="Tide">Tide</option>
36
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galaxyp
parents: 35
diff changeset
458 <option value="MyriMatch">MyriMatch</option>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
459 <option value="MS_Amanda">MS_Amanda</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
460 <!-- Windows only
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
461 <option value="Andromeda">Andromeda</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
462 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
463 <!-- New with version 3.0
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
464 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
465 <!--working in tests
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
466 -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
467 <option value="DirecTag">DirecTag</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
468 <option value="Novor">Novor (Select for non-commercial use only)</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
469 <validator type="no_options" message="Please select at least one output file" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
470 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
471 </section>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
472
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
473
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
474 <!-- General Parameters -->
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
475 <expand macro="general_options"/>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
476
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
477
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
478 <section name="advanced_options" expanded="false" title="Andvanced Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
479 <!-- Optional Advanced SearchGUI Parameters -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
480 <conditional name="searchgui_advanced">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
481 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
482 <option value="basic" selected="True">Default</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
483 <option value="advanced">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
484 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
485 <when value="basic" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
486 <when value="advanced">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
487 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
488 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
489 <option value="0">no correction</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
490 <option value="1" selected="True">rename spectra</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
491 <option value="2">delete spectra</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
492 </param>
36
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galaxyp
parents: 35
diff changeset
493
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
494 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
495 label="Add missing spectrum titles" help="(-missing_titles)"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
496
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
497 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
498 help="Choose a smaller value if you are running on a machine with limited memory"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
499
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
500 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
501 help="Choose a smaller value if you are running on a machine with limited memory"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
502 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
503 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
504
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
505 <!-- X!TANDEM ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
506 <conditional name="xtandem">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
507 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
508 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
509 <option value="no" selected="True">Default</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
510 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
511 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
512 <when value="yes">
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
513 <param name="xtandem_npeaks" type="integer" value="50"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
514 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
515 <param name="xtandem_min_peaks" type="integer" value="15"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
516 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
517 <param name="xtandem_min_frag_mz" type="integer" value="200"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
518 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
519 <param name="xtandem_min_prec_mass" type="integer" value="200"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
520 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
521 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
522 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
523 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
524 label="X!Tandem: Dynamic Range" value="100" type="integer" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
525 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
526 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
527 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
528 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
529 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
530 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
531 <param name="xtandem_evalue" help="Highest value for recorded peptides"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
532 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
533 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
534 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
535 <param name="xtandem_output_sequences" help="Controls output of sequence information"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
536 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
537 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
538 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
34
2439164e6061 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit dea56622eb32b82c87dc87567dc89db3a787033d
galaxyp
parents: 33
diff changeset
539 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
540
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
541 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
542 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
543 <option value="no" selected="True">Don't refine</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
544 <option value="yes" >Use refinement</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
545 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
546 <when value="no"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
547 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
548 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
549 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
550 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
551 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
552 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
553 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
554 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
555 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
556 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
557 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
558 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
559 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
560 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
561 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
562 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
563 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
564 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
565 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
566
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
567 <!-- OMSSA ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
568 <conditional name="omssa">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
569 <param name="omssa_advanced" type="select" label="OMSSA Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
570 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
571 <option value="no" selected="True">Default</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
572 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
573 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
574 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
575 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
576 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
577 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
578 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
579
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
580 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
581 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
582 <param name="omssa_neutron" type="float" value="1446.94"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
583 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
584 <param name="omssa_low_intensity" type="float" value="0.0"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
585 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
36
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galaxyp
parents: 35
diff changeset
586 <param name="omssa_high_intensity" type="float" value="0.2"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
587 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
588 <param name="omssa_intensity_incr" type="float" value="0.0005"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
589 label="OMSSA: Intensity Increment" help="Intensity increment" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
590 <param name="omssa_single_window_wd" type="integer" value="27"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
591 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
592 <param name="omssa_double_window_wd" type="integer" value="14"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
593 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
594 <param name="omssa_single_window_pk" type="integer" value="2"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
595 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
596 <param name="omssa_double_window_pk" type="integer" value="2"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
597 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
598 <param name="omssa_min_ann_int_pks" type="integer" value="6"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
599 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
600 <param name="omssa_min_annotated_peaks" type="integer" value="2"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
601 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
602 <param name="omssa_min_peaks" type="integer" value="4"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
603 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
604 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
605 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
606 <param name="omssa_max_ladders" type="integer" value="128"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
607 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
608 <param name="omssa_max_frag_charge" type="integer" value="2"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
609 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
610 <param name="omssa_fraction" type="float" value="0.95"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
611 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
612 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
613 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
614 <param name="omssa_charge" type="select"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
615 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
616 <option value="0" >Minus</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
617 <option value="1" selected="True">Plus</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
618 </param>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
619 <param name="omssa_prec_per_spectrum" type="integer" value="1"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
620 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
621 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
622 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
623 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
624 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
625 <param name="omssa_max_frag_series" type="integer" value="100"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
626 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
627 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
628 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
629 <param name="omssa_consecutive_p" type="float" value="0.5"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
630 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
631 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
632 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
633 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
634 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
635 <param name="omssa_it_replace_evalue" type="float" value="0.01"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
636 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
637 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
638 label="OMSSA: Remove Precursor" help="Remove precursors" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
639 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
640 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
641 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
642 label="OMSSA: Remove Precursor" help="Remove precursors" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
643 <param name="omssa_max_evalue" type="float" value="100"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
644 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
645 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
646 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
647 <param name="omssa_it_replace_evalue" type="float" value="100"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
648 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
649 <param name="omssa_hitlist_length" type="integer" value="0"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
650 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
651 <param name="omssa_hitlist_charge" type="integer" value="30"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
652 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
653 <param name="omssa_min_pep_length" type="integer" value="4"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
654 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
655 <param name="omssa_max_pep_length" type="integer" value="40"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
656 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
657 <param name="omssa_format" label="OMSSA output format" type="select" >
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
658 <option value="0" selected="True">OMX</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
659 <option value="1" >CSV</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
660 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
661 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
662 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
663
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
664 <!-- MS-GF+ ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
665 <conditional name="msgf">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
666 <param name="msgf_advanced" type="select" label="MSGF Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
667 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
668 <option value="no" selected="True">Default</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
669 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
670 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
671 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
672 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
673 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
674 <param name="msgf_min_pep_length" type="integer" value="6"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
675 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
676 <param name="msgf_max_pep_length" type="integer" value="30"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
677 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
678 <param name="msgf_termini" type="select" format="txt"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
679 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
680 <option value="0">0 (ie non-specific cleavage)</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
681 <option value="1">1 (ie semi-tryptic cleavage)</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
682 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
683 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
684 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
685
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
686 <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)">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
687 <option value="0" selected="True">Low-res LCQ/LTQ</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
688 <option value="1" >High-res LTQ</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
689 <option value="2" >TOF</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
690 <option value="3" >Q-Exactive</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
691 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
692 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
693 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
694 <option value="1" >CID</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
695 <option value="2" >ETD</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
696 <option value="3" >HCD</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
697 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
698 <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">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
699 <option value="0" selected="True">Automatic</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
700 <option value="1" >Phosphorylation</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
701 <option value="2" >iTRAQ</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
702 <option value="3" >iTRAQPhospho</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
703 <option value="4" >TMT</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
704 <option value="5" >Standard</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
705 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
706 <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" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
707 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
708 <option value="0" selected="True">output basic scores only</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
709 <option value="1" >output additional features</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
710 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
711 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
712 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
713
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
714 <!-- MS-AMANDA ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
715 <conditional name="ms_amanda">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
716 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
717 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
718 <option value="no" selected="True">Default</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
719 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
720 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
721 <when value="yes">
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
722 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
723 label="MS Amanda: Generate Decoys" help="generate decoys" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
724 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
725 help="MS Amanda instrument id option. Available ion types are listed here.">
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
726
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
727 <option value="b, y" selected="True">b, y</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
728 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
729 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
730 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
731 <option value="a, b, y" >a, b, y</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
732 <option value="a, b, y, Imm" >a, b, y, Imm</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
733 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
734 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
735 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
736 <option value="b, y, INT" >b, y, INT</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
737 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
738 <option value="a, b, y, INT" >a, b, y, INT</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
739 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
740 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
741 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
742 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
743
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
744 </param>
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
745 <param name="ms_amanda_max_rank" type="integer" value="10"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
746 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
747 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
748 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
749 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
750 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
751
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
752
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
753 <!-- TIDE ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
754 <conditional name="tide">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
755 <param name="tide_advanced" type="select" label="TIDE Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
756 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
757 <option value="no" selected="True">Default</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
758 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
759 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
760 <when value="yes">
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
761 <param name="tide_num_ptms" type="integer" value="" optional="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
762 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
763 <param name="tide_num_ptms_per_type" type="integer" value="2"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
764 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
765 <param name="tide_min_pep_length" type="integer" value="6"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
766 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
767 <param name="tide_max_pep_length" type="integer" value="30"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
768 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
769 <param name="tide_min_prec_mass" type="float" value="200.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
770 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
771 <param name="tide_max_prec_mass" type="float" value="7200.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
772 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
773 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
774 <option value="none" selected="True">none</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
775 <option value="shuffle" >shuffle</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
776 <option value="peptide-revers" >peptide-reverse</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
777 <option value="protein-reverse" >protein-reverse</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
778 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
779 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
780 <option value="N" >N</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
781 <option value="C" >C</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
782 <option value="NC" selected="True">NC</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
783 <option value="non" >none</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
784 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
785 <param name="tide_decoy_seed" type="integer" value="1"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
786 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
787 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
788 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
789 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
790 <option value="0" >0</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
791 <option value="10" >10</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
792 <option value="20" >20</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
793 <option value="30" selected="True">30</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
794 <option value="40" >40</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
795 <option value="50" >50</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
796 <option value="60" >60</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
797 </param>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
798
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
799 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
800 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
801 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
802 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
803 <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">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
804 <option value="full-digest" selected="True">full-digest</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
805 <option value="partial-digest" >partial-digest</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
806 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
807 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
808 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
809 <param name="tide_max_psms" type="integer" value="10"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
810 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
811 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
812 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
813 <param name="tide_min_spectrum_mz" type="float" value="0.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
814 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
815 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
816 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
817 <param name="tide_min_spectrum_peaks" type="integer" value="20"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
818 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
819 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
820 <option value="1" >1</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
821 <option value="2" >2</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
822 <option value="3" >3</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
823 <option value="all" selected="True">all</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
824 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
825 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
826 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
827 <param name="tide_remove_prec_tol" type="float" value="1.5"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
828 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
829 <param name="tide_progress_indicator" type="integer" value="1000"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
830 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
831 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
832 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
833 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
834 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
835 <param name="tide_mz_bin_width" type="float" value="0.02"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
836 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
837 <param name="tide_mz_bin_offset" type="float" value="0.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
838 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
839 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
840 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
841
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
842 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
843 <option value="tide_export_text" selected="True">Text</option>
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
844 <option value="tide_export_sqt" >SQT</option>
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
845 <option value="tide_export_pepxml" >pepxml</option>
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
846 <option value="tide_export_mzid" >MzIdentML</option>
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
847 <option value="tide_export_pin" >Percolator input file</option>
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
848 </param>
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
849
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
850 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
851 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
852 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
853 </conditional>
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
854
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
855
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
856 <!-- MyriMatch ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
857 <conditional name="myrimatch">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
858 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
859 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
860 <option value="no" selected="True">Default</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
861 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
862 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
863 <when value="yes">
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
864 <param name="myrimatch_min_pep_length" type="integer" value="8"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
865 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
866 <param name="myrimatch_max_pep_length" type="integer" value="30"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
867 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
868 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
869 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
870 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
871 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
872 <param name="myrimatch_num_matches" type="integer" value="10"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
873 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
874 <param name="myrimatch_num_ptms" type="integer" value="2"
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
875 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
876 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
877 <option value="CID" selected="True">CID</option>
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
878 <option value="HCD" >HCD</option>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
879 <option value="ETD" >ETD</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
880 </param>
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
881 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
882 <option value="0">None required</option>
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
883 <option value="1">At least one</option>
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
884 <option value="2" selected="True" >Both</option>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
885 </param>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
886 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
887 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
888 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
889 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
890 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
891 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)" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
892 <param name="myrimatch_intensity_classes" type="integer" value="3"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
893 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
894 <param name="myrimatch_class_multiplier" type="integer" value="2"
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
895 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" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
896 <param name="myrimatch_num_batches" type="integer" value="50"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
897 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
898 <param name="myrimatch_max_peak" type="integer" value="100"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
899 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
900 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
901 </conditional>
38
263440bb1900 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
galaxyp
parents: 37
diff changeset
902
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
903
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
904 <!-- Andromeda ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
905 <!-- Windows only
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
906 <conditional name="andromeda">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
907 <param name="andromeda_advanced" type="select" label="Andromeda Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
908 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
909 <option value="no" selected="True">Default</option>
15
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
910 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
911 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
912 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
913 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
914 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
915 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
916 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
917 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
918 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
919 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
920 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
921 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
922 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
923 <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" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
924 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
925 <option value="CID" selected="true">CID</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
926 <option value="HCD">HCD</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
927 <option value="EDT">EDT</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
928 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
929 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
930 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
931 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
932 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
933 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
934 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
935 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
936 -->
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
937
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
938 <!-- Comet ADVANCED PARAMETERS -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
939 <conditional name="comet">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
940 <param name="comet_advanced" type="select" label="Comet Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
941 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
942 <option value="no" selected="True">Default</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
943 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
944 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
945 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
946 <!-- Spectrum Related parameters -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
947 <conditional name="comet_spectrum">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
948 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
949 <option value="yes">Set Spectrum Parameters</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
950 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
951 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
952 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
953 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
954 <param name="comet_min_peaks" type="integer" value="10"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
955 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
956 <param name="comet_min_peak_int" type="float" value="0.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
957 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
958 <conditional name="comet_prec">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
959 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
960 <option value="0" selected="True" >off</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
961 <option value="1">on</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
962 <option value="2">as expected for ETD/ECD spectra</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
963 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
964 <when value="0" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
965 <when value="1">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
966 <param name="comet_remove_prec_tol" type="float" value="1.5"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
967 label="Comet: Remove Precursor Tolerance" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
968 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
969 <when value="2">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
970 <param name="comet_remove_prec_tol" type="float" value="1.5"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
971 label="Comet: Remove Precursor Tolerance" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
972 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
973 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
974 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
975 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" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
976 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
36
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galaxyp
parents: 35
diff changeset
977 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" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
978 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
979 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
980 <!-- Search Related parameters -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
981 <conditional name="comet_search">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
982 <param name="comet_search_selector" type="select" label="Comet: Search Related">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
983 <option value="yes">Set Search Parameters</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
984 <option value="no" selected="True">Keep Default Search Parameters</option>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
985 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
986 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
987 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
988 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
989 <option value="1">semi-specific</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
990 <option value="2" selected="True">full-enzyme</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
991 <option value="8">unspecific N-term</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
992 <option value="9">unspecific C-term</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
993 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
994 <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">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
995 <option value="0" selected="True">off</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
996 <option value="1">-1,0,+1,+2,+3</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
997 <option value="2">-8,-4,0,+4,+8</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
998 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
999 <param name="comet_min_prec_mass" type="float" value="0.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1000 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1001 <param name="comet_max_prec_mass" type="float" value="10000.0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1002 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1003 <param name="comet_num_matches" type="integer" value="10"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1004 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1005 <param name="comet_max_frag_charge" type="integer" value="3"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1006 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
1007 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1008 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1009 <param name="comet_batch_size" type="integer" value="0"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1010 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" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1011 <param name="comet_num_ptms" type="integer" value="10"
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
1012 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1013 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1014 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1015 <!-- Fragment Ions Related parameters -->
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1016 <conditional name="comet_fragment_ions">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1017 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1018 <option value="yes">Set Fragment Ions Parameters</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1019 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1020 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1021 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1022 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1023 <param name="comet_frag_bin_offset" type="float" value="0.4"
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1024 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1025 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
1026 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1027 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1028 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1029 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1030 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1031 <conditional name="directtag">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1032 <param name="directtag_advanced" type="select" label="DirectTag Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1033 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1034 <option value="no" selected="True">Default</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1035 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1036 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1037 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1038 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1039 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1040 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1041 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1042 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1043 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1044 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1045 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1046 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1047 <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."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1048 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1049 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1050 <option value="0" selected="true">no deisotoping</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1051 <option value="1">precursor only</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1052 <option value="2">precursor and candidate</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
1053 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1054 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1055 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1056 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1057 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1058 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1059 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1060 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1061 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1062 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1063 </conditional>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
1064
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1065 <conditional name="novor">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1066 <param name="novor_advanced" type="select" label="Novor Options">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1067 <option value="yes">Advanced</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1068 <option value="no" selected="True">Default</option>
18
ffed32e397cb Uploaded
galaxyp
parents: 17
diff changeset
1069 </param>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1070 <when value="no" />
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1071 <when value="yes">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1072 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1073 <option value="HCD" selected="True">HCD</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1074 <option value="CID">CID</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1075 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1076 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1077 <option value="FT" selected="True">FT</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1078 <option value="Trap" >Trap</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1079 <option value="TOF" >TOF</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1080 </param>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1081 </when>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1082 </conditional>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
1083 </section>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1084 </inputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1085 <outputs>
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
1086 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1087 </outputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1088 <tests>
9
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iracooke
parents: 7
diff changeset
1089
11
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iracooke
parents: 10
diff changeset
1090 <!-- Test that specifying non-default search engines works -->
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1091 <test>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
1092 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
1093 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1094 <param name="precursor_ion_tol" value="100"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1095 <param name="fixed_modifications" value="carbamidomethyl c"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1096 <param name="variable_modifications" value="oxidation of m"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1097 <param name="min_charge" value="1"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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parents:
diff changeset
1098 <param name="max_charge" value="3"/>
9
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iracooke
parents: 7
diff changeset
1099 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1
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iracooke
parents: 0
diff changeset
1100 <param name="xtandem.xtandem_advanced" value="yes"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
1101 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
36
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parents: 35
diff changeset
1102 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
1103 </test>
11
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iracooke
parents: 10
diff changeset
1104 <!-- Test that search works with MSAmanda -->
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1105 <test>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1106 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1107 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
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iracooke
parents: 10
diff changeset
1108 <param name="precursor_ion_tol" value="100"/>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1109 <param name="fixed_modifications" value="carbamidomethyl c"/>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1110 <param name="variable_modifications" value="oxidation of m"/>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
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diff changeset
1111 <param name="min_charge" value="1"/>
76d14dc397ed planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 10
diff changeset
1112 <param name="max_charge" value="3"/>
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diff changeset
1113 <param name="engines" value="MS_Amanda"/>
36
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diff changeset
1114 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
11
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diff changeset
1115 </test>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
1116 </tests>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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1117 <help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
1118 **What it does**
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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1119
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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1120 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
6
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diff changeset
1121 Default: X! Tandem, OMSSA and MS-GF+ are executed.
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diff changeset
1122 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
0
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1123
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diff changeset
1124 </help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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diff changeset
1125 <expand macro="citations" />
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1126 </tool>