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annotate searchgui.xml @ 1:cb1666df2fb3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
author iracooke
date Wed, 03 Jun 2015 14:01:07 -0400
parents a9e90cdcb97a
children 843dba58aa7c
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cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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1 <tool id="search_gui" name="Search GUI" version="1.28.0">
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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 <requirements>
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6 <requirement type="package" version="1.28">searchgui</requirement>
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7 </requirements>
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8 <macros>
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9 <import>macros.xml</import>
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10 </macros>
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11 <expand macro="stdio" />
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12 <command>
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13 <![CDATA[
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14 #from datetime import datetime
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15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 #set $temp_stderr = "searchgui_stderr"
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19 mkdir output;
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20 mkdir output_reports;
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21 cwd=`pwd`;
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22 #for $mgf in $peak_lists:
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23 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
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24 ln -s -f '${mgf}' '${input_name}';
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25 #end for
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26 ##ln -s "${input_database}" input_database.fasta;
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27 cp "${input_database}" input_database.fasta;
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29 ###########################################
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30 #### Creating decoy database ####
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31 ###########################################
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32 #if $create_decoy:
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33 echo "Creating decoy database.";
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34 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
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35 rm input_database.fasta &&
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36 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
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37 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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38 #end if
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40 #####################################################
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41 ## generate IdentificationParameters for SearchGUI ##
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42 #####################################################
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44 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
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45 -out SEARCHGUI_IdentificationParameters.parameters
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47 @GENERAL_PARAMETERS@
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49 -db input_database.fasta
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51 #if $xtandem.xtandem_advanced == "yes"
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52
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53 -xtandem_npeaks ${xtandem.xtandem_npeaks}
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54 -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
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55 -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}
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56 -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}
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57 -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}
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58 -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}
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59 -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl}
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60 -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro}
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61 -xtandem_stp_bias ${xtandem.xtandem_stp_bias}
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62 -xtandem_evalue ${xtandem.xtandem_evalue}
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63 -xtandem_output_proteins ${xtandem.xtandem_output_proteins}
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64 -xtandem_output_sequences ${xtandem.xtandem_output_sequences}
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65 -xtandem_output_spectra ${xtandem.xtandem_output_spectra}
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66 ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}
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67
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68 #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
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69 -xtandem_refine 1
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70 -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}
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71 -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}
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72 -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}
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73 -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}
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74 -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
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75 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
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76 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
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77
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78 #end if
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79 #end if
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80
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
81 #if $omssa.omssa_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
82 -omssa_hitlist_length ${omssa.hitlist_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
83 -omssa_remove_prec ${omssa.remove_precursor}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
84 -omssa_scale_prec ${omssa.scale_precursor}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
85 -omssa_estimate_charge ${omssa.estimate_charge}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
86
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
87 -omssa_memory ${omssa.omssa_memory}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
88 -omssa_isotopes ${omssa.omssa_isotopes}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
89 -omssa_neutron ${omssa.omssa_neutron}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
90 -omssa_low_intensity "${omssa.omssa_low_intensity}"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
91 -omssa_high_intensity ${omssa.omssa_high_intensity}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
92 -omssa_intensity_incr ${omssa.omssa_intensity_incr}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
93 -omssa_single_window_wd ${omssa.omssa_single_window_wd}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
94 -omssa_double_window_wd ${omssa.omssa_double_window_wd}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
95 -omssa_single_window_pk ${omssa.omssa_single_window_pk}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
96 -omssa_double_window_pk ${omssa.omssa_double_window_pk}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
97 -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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98 -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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99 -omssa_min_peaks ${omssa.omssa_min_peaks}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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100 -omssa_methionine ${omssa.omssa_methionine}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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101 -omssa_max_ladders ${omssa.omssa_max_ladders}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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102 -omssa_max_frag_charge ${omssa.omssa_max_frag_charge}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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103 -omssa_fraction ${omssa.omssa_fraction}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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104 -omssa_plus_one ${omssa.omssa_plus_one}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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105 -omssa_charge ${omssa.omssa_charge}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
106 -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
107 -omssa_forward ${omssa.omssa_forward}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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108 -omssa_rewind ${omssa.omssa_rewind}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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109 -omssa_max_frag_series ${omssa.omssa_max_frag_series}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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110 -omssa_corr ${omssa.omssa_corr}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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111 -omssa_consecutive_p ${omssa.omssa_consecutive_p}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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112 -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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113 -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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114 -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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115 -omssa_max_evalue ${omssa.omssa_max_evalue}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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116 -omssa_hitlist_charge ${omssa.omssa_hitlist_charge}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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117 -omssa_min_pep_length ${omssa.omssa_min_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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118 -omssa_max_pep_length ${omssa.omssa_max_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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119 -omssa_format ${omssa.omssa_format}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
120 #end if
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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121
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
122 #if $msgf.msgf_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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123 -msgf_decoy ${msgf.msgf_decoy}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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124 -msgf_min_pep_length ${msgf.msgf_min_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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125 -msgf_max_pep_length ${msgf.msgf_max_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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126 -msgf_termini ${msgf.msgf_termini}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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127 -msgf_num_ptms ${msgf.msgf_num_ptms}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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128 -msgf_instrument ${msgf.msgf_instrument}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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129 -msgf_fragmentation ${msgf.msgf_fragmentation}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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130 -msgf_protocol ${msgf.msgf_protocol}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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131 -msgf_num_matches ${msgf.msgf_num_matches}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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132 -msgf_additional ${msgf.msgf_additional}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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133 -msgf_isotope_low ${msgf.msgf_isotope_low}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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134 -msgf_isotope_high ${msgf.msgf_isotope_high}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
135 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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136
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
137 #if $ms_amanda.ms_amanda_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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138 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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139 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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140 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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141 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
142 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
143 # end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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diff changeset
144
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
145 #if $myrimatch.myrimatch_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
146 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
147 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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148 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
149 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
150 -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
151 -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
152 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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153 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
154 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
155 -myrimatch_termini ${myrimatch.myrimatch_termini}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
156 -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
157 -myrimatch_xcorr ${myrimatch.myrimatch_xcorr}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
158 -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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159 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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160 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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161 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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162 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
163 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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164
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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diff changeset
165 #if $tide.tide_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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166 -tide_num_ptms ${tide.tide_num_ptms}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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167 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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168 -tide_min_pep_length ${tide.tide_min_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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169 -tide_max_pep_length ${tide.tide_max_pep_length}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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170 -tide_min_prec_mass ${tide.tide_min_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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171 -tide_max_prec_mass ${tide.tide_max_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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172 -tide_decoy_format ${tide.tide_decoy_format}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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173 -tide_keep_terminals ${tide.tide_keep_terminals}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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174
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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175 -tide_output_folder ${tide.tide_output_folder}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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176 -tide_print_peptides ${tide.tide_print_peptides}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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177 -tide_verbosity ${tide.tide_verbosity}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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178 -tide_monoisotopic ${tide.tide_monoisotopic}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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179 -tide_clip_n_term ${tide.tide_clip_n_term}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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180 -tide_digestion_type ${tide.tide_digestion_type}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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181 -tide_compute_sp ${tide.tide_compute_sp}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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182 -tide_max_psms ${tide.tide_max_psms}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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183 -tide_compute_p ${tide.tide_compute_p}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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184 -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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185 -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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186 -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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187 -tide_spectrum_charges ${tide.tide_spectrum_charges}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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188 -tide_remove_prec ${tide.tide_remove_prec}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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189 -tide_remove_prec_tol ${tide.tide_remove_prec_tol}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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190 -tide_progress_indicator ${tide.tide_progress_indicator}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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191 -tide_use_flanking ${tide.tide_use_flanking}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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192 -tide_use_neutral_losses ${tide.tide_use_neutral_losses}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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193 -tide_mz_bin_width ${tide.tide_mz_bin_width}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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194 -tide_mz_bin_offset ${tide.tide_mz_bin_offset}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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195 -tide_concat ${tide.tide_concat}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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196 -tide_export_text ${tide.tide_export_text}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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197 -tide_export_sqt ${tide.tide_export_sqt}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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198 -tide_export_pepxml ${tide.tide_export_pepxml}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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199 -tide_export_mzid ${tide.tide_export_mzid}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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200 -tide_export_pin ${tide.tide_export_pin}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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201 -tide_remove_temp ${tide.tide_remove_temp}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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202 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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203
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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204
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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205 #if $comet.comet_advanced == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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206
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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207 #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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208 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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209 -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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210 -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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211
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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212
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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213 #if $comet.comet_spectrum.comet_remove_prec == "1"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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214 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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215 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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216
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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217 #if $comet.comet_spectrum.comet_remove_prec == "2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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218 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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219 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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220
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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221 -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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222 -comet_clear_mz_range_upper ${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
galaxyp
parents:
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223 #end if
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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224
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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225 #if $comet.comet_search.comet_search_selector == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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226 -comet_enzyme_type ${comet.comet_search.comet_enzyme_type}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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227 -comet_isotope_correction ${comet.comet_search.comet_isotope_correction}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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228 -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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229 -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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230 -comet_num_matches ${comet.comet_search.comet_num_matches}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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231 -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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232 -comet_remove_meth ${comet.comet_search.comet_remove_meth}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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233 -comet_batch_size ${comet.comet_search.comet_batch_size}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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234 -comet_num_ptms ${comet.comet_search.comet_num_ptms}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
235 #end if
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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236
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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237 #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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238 -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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239 -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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240 -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
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241
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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242 #end if
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243
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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244 #end if
0
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245
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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246 2> $temp_stderr)
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247 &&
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248
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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249 ################
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250 ## Search CLI ##
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251 ################
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252 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
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253 -temp_folder `pwd`
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254 -spectrum_files \$cwd
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255 -output_folder \$cwd/output
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256 -id_params SEARCHGUI_IdentificationParameters.parameters
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257
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258 -threads "\${GALAXY_SLOTS:-12}"
1
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259
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260 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
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261 -correct_titles "${searchgui_advanced.correct_titles}"
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262 $searchgui_advanced.missing_titles
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263 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
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264 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
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265 #end if
0
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266
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267 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
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268 ## the tree is generated afterwards in PeptideShaker
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269 -protein_index 0
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270
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271 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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272
1
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273 #set $engines_list = str($engines).split(',')
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274 #if 'X!Tandem' in $engines_list:
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275 ##if str($XTANDEM_selector) == 'True'
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276 -xtandem 1
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277 #else
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278 -xtandem 0
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279 #end if
0
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280
1
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281 #if 'MyriMatch' in $engines_list:
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282 ##if str($MYRIMATCH_selector) == "True"
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283 -myrimatch 1
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284 #else
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285 -myrimatch 0
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286 #end if
0
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287
1
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288 #if 'MSGF' in $engines_list:
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289 ##if str($MSGF_selector) == "True"
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290 -msgf 1
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291 #else
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292 -msgf 0
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293 #end if
0
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294
1
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295 #if 'OMSSA' in $engines_list:
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296 ##if str($OMSSA_selector) == "True"
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297 -omssa 1
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298 #else
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299 -omssa 0
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300 #end if
0
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301
1
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302 #if 'Comet' in $engines_list:
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303 ##if str($COMET_selector) == "True"
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304 -comet 1
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305 #else
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306 -comet 0
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307 #end if
0
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308
1
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309 #if 'Tide' in $engines_list:
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310 ##if str($TIDE_selector) == "True"
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311 -tide 1
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312 #else
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313 -tide 0
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314 #end if
0
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315
1
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316 #if 'MS_Amanda' in $engines_list:
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317 -ms_amanda 1
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318 #else
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319 -ms_amanda 0
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320 #end if
0
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321
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322 ## single zip file
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323 -output_option 0
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324
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325 ## mgf and database in output
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326 -output_data 1
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327
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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328 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
329
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
330 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
331
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
332 (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
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333
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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334 &&
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
335
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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336 exit_code_for_galaxy=\$?;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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337 cat $temp_stderr 2>&1;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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338 (exit \$exit_code_for_galaxy)
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
339 ]]>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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340 </command>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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341 <inputs>
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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342
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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343 <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
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344 help="Select FASTA database from history"/>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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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 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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347 label="Create a concatenated target/decoy database before running PeptideShaker"
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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348 help="Selecting this option will help PeptideShaker calculate FDR values" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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349
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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350 <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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351 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
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352
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
353 <!-- Search Engine Selection -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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354 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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355 <option value="X!Tandem" selected="True">X!Tandem</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
356 <option value="MyriMatch">MyriMatch</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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diff changeset
357 <option value="MS_Amanda">MS_Amanda</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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358 <option value="MSGF" selected="True">MS-GF+</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
359 <option value="OMSSA" selected="True">OMSSA</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
360 <option value="Comet">Comet</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
361 <option value="Tide">Tide</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
362 <validator type="no_options" message="Please select at least one output file" />
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
363 </param>
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
364
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
365
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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366
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
367 <!-- General Parameters -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
368 <expand macro="general_options"/>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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369
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
370 <!-- Optional Advanced SearchGUI Parameters -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
371 <conditional name="searchgui_advanced">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
372 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
373 <option value="basic" selected="True">Default</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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374 <option value="advanced">Advanced</option>
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
375 </param>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
376 <when value="basic" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
377 <when value="advanced">
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
378 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
379 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
380 <option value="0">no correction</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
381 <option value="1" selected="True">rename spectra</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
382 <option value="2">delete spectra</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
383 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
384
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
385 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
386 label="Add missing spectrum titles" help="(-missing_titles)"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
387
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
388 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
389 help="Choose a smaller value if you are running on a machine with limited memory"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
390
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
391 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
392 help="Choose a smaller value if you are running on a machine with limited memory"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
393 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
394 </conditional>
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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395
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
396
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
397 <!-- X!TANDEM ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
398 <conditional name="xtandem">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
399 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
400 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
401 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
402 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
403 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
404 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
405 <param name="xtandem_npeaks" type="integer" value="50"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
406 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
407 <param name="xtandem_min_peaks" type="integer" value="15"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
408 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
409 <param name="xtandem_min_frag_mz" type="integer" value="200"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
410 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
411 <param name="xtandem_min_prec_mass" type="integer" value="200"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
412 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
413 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
414 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
415 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
416 label="X!Tandem: Dynamic Range" value="100" type="integer" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
417 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
418 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
419 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
420 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
421 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
422 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
423 <param name="xtandem_evalue" help="Highest value for recorded peptides"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
424 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
425 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
426 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
427 <param name="xtandem_output_sequences" help="Controls output of sequence information"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
428 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
429 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
430 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
431 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
432
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
433 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
434 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
435 <option value="no" selected="True">Don't refine</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
436 <option value="yes" >Use refinement</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
437 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
438 <when value="no"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
439 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
440 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
441 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
442 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
443 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
444 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
445 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
446 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
447 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
448 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
449 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
450 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
451 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
452 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
453 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
454 </when>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
455 </conditional>
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
456 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
457 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
458
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
459 <!-- OMSSA ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
460 <conditional name="omssa">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
461 <param name="omssa_advanced" type="select" label="OMSSA Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
462 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
463 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
464 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
465 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
466 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
467 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
468 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
469 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
470 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
471
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
472 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
473 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
474 <!-- param name="omssa_isotopes" type="integer" value="0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
475 label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
476 <param name="omssa_neutron" type="float" value="1446.94"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
477 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
478 <param name="omssa_low_intensity" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
479 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
480 <param name="omssa_high_intensity" type="float" value="0.2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
481 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
482 <param name="omssa_intensity_incr" type="float" value="0.0005"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
483 label="OMSSA: Intensity Increment" help="Intensity increment" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
484 <param name="omssa_single_window_wd" type="integer" value="27"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
485 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
486 <param name="omssa_double_window_wd" type="integer" value="14"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
487 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
488 <param name="omssa_single_window_pk" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
489 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
490 <param name="omssa_double_window_pk" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
491 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
492 <param name="omssa_min_ann_int_pks" type="integer" value="6"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
493 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
494 <param name="omssa_min_annotated_peaks" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
495 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
496 <param name="omssa_min_peaks" type="integer" value="4"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
497 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
498 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
499 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
500 <param name="omssa_max_ladders" type="integer" value="128"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
501 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
502 <param name="omssa_max_frag_charge" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
503 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
504 <param name="omssa_fraction" type="float" value="0.95"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
505 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
506 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
507 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
508 <param name="omssa_charge" type="select"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
509 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
510 <option value="0" >Minus</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
511 <option value="1" selected="True">Plus</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
512 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
513 <param name="omssa_prec_per_spectrum" type="integer" value="1"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
514 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
515 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
516 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
517 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
518 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
519 <param name="omssa_max_frag_series" type="integer" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
520 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
521 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
522 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
523 <param name="omssa_consecutive_p" type="float" value="0.5"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
524 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
525 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
526 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
527 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
528 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
529 <param name="omssa_it_replace_evalue" type="float" value="0.01"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
530 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
531 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
532 label="OMSSA: Remove Precursor" help="Remove precursors" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
533 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
534 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
535 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
536 label="OMSSA: Remove Precursor" help="Remove precursors" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
537 <param name="omssa_max_evalue" type="float" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
538 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
539 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
540 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
541 <param name="omssa_it_replace_evalue" type="float" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
542 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
543 <param name="omssa_hitlist_length" type="integer" value="0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
544 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
545 <param name="omssa_hitlist_charge" type="integer" value="30"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
546 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
547 <param name="omssa_min_pep_length" type="integer" value="4"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
548 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
549 <param name="omssa_max_pep_length" type="integer" value="40"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
550 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
551 <param name="omssa_format" label="OMSSA output format" type="select" >
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
552 <option value="0" selected="True">OMX</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
553 <option value="1" >CSV</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
554 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
555
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
556 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
557 </conditional>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
558
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
559 <!-- MS-GF+ ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
560 <conditional name="msgf">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
561 <param name="msgf_advanced" type="select" label="MSGF Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
562 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
563 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
564 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
565 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
566 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
567 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
568 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
569 <param name="msgf_min_pep_length" type="integer" value="6"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
570 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
571 <param name="msgf_max_pep_length" type="integer" value="30"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
572 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
573 <param name="msgf_termini" type="select" format="text"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
574 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
575 <option value="0">0 (ie non-specific cleavage)</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
576 <option value="1">1 (ie semi-tryptic cleavage)</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
577 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
578 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
579 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
580
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
581 <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)">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
582 <option value="0" selected="True">Low-res LCQ/LTQ</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
583 <option value="1" >High-res LTQ</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
584 <option value="2" >TOF</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
585 <option value="3" >Q-Exactive</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
586 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
587 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
588 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
589 <option value="1" >CID</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
590 <option value="2" >ETD</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
591 <option value="3" >HCD</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
592 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
593 <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">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
594 <option value="0" selected="True">Automatic</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
595 <option value="1" >Phosphorylation</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
596 <option value="2" >iTRAQ</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
597 <option value="3" >iTRAQPhospho</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
598 <option value="4" >TMT</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
599 <option value="5" >Standard</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
600 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
601 <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" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
602 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
603 <option value="0" selected="True">output basic scores only</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
604 <option value="1" >output additional features</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
605 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
606 <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
607 <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
608 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
609 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
610
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
611 <!-- MS-AMANDA ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
612 <conditional name="ms_amanda">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
613 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
614 <option value="yes" selected="True">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
615 <option value="no">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
616 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
617 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
618 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
619 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
620 label="MS Amanda: Generate Decoys" help="generate decoys" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
621 <param name="ms_amanda_max_evalue" type="float" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
622 label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
623 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
624 <param name="ms_amanda_max_rank" type="integer" value="5"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
625 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
626 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
627 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
628 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
629 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
630
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
631
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
632 <!-- TIDE ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
633 <conditional name="tide">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
634 <param name="tide_advanced" type="select" label="TIDE Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
635 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
636 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
637 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
638 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
639 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
640 <param name="tide_num_ptms" type="integer" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
641 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
642 <param name="tide_num_ptms_per_type" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
643 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
644 <param name="tide_min_pep_length" type="integer" value="6"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
645 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
646 <param name="tide_max_pep_length" type="integer" value="30"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
647 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
648 <param name="tide_min_prec_mass" type="float" value="200.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
649 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
650 <param name="tide_max_prec_mass" type="float" value="7200.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
651 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
652 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
653 <option value="none" selected="True">none</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
654 <option value="shuffle" >shuffle</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
655 <option value="peptide-revers" >peptide-reverse</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
656 <option value="protein-reverse" >protein-reverse</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
657 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
658 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
659 <option value="N" >N</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
660 <option value="C" >C</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
661 <option value="NC" selected="True">NC</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
662 <option value="non" >none</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
663 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
664 <param name="tide_decoy_seed" type="integer" value="1"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
665 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
666 <param name="tide_output_folder" type="text" value="crux-output"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
667 label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
668 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
669 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
670 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
671 <option value="0" >0</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
672 <option value="10" >10</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
673 <option value="20" >20</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
674 <option value="30" selected="True">30</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
675 <option value="40" >40</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
676 <option value="50" >50</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
677 <option value="60" >60</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
678 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
679
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
680 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
681 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
682 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
683 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
684 <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">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
685 <option value="full-digest" selected="True">full-digest</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
686 <option value="partial-digest" >partial-digest</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
687 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
688 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
689 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
690 <param name="tide_max_psms" type="integer" value="10"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
691 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
692 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
693 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
694 <param name="tide_min_spectrum_mz" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
695 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
696 <param name="tide_max_spectrum_mz" type="float" value="100000.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
697 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
698 <param name="tide_min_spectrum_peaks" type="integer" value="20"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
699 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
700 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
701 <option value="1" >1</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
702 <option value="2" >2</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
703 <option value="3" >3</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
704 <option value="all" selected="True">all</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
705 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
706 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
707 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
708 <param name="tide_remove_prec_tol" type="float" value="1.5"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
709 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
710 <param name="tide_progress_indicator" type="integer" value="1000"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
711 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
712 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
713 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
714 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
715 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
716 <param name="tide_mz_bin_width" type="float" value="0.02"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
717 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
718 <param name="tide_mz_bin_offset" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
719 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
720 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
721 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
722 <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
723 label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
724 <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
725 label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
726 <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
727 label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
728 <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
729 label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
730 <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
731 label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
732 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
733 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
734 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
735 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
736
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
737 <!-- MyriMatch ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
738 <conditional name="myrimatch">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
739 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
740 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
741 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
742 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
743 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
744 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
745 <param name="myrimatch_min_pep_length" type="integer" value="6"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
746 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
747 <param name="myrimatch_max_pep_length" type="integer" value="30"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
748 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
749 <param name="myrimatch_min_prec_mass" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
750 label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
751 <param name="myrimatch_max_prec_mass" type="float" value="10000.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
752 label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
753 <param name="myrimatch_isotope_low" type="integer" value="-1"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
754 label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
755 <param name="myrimatch_isotope_high" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
756 label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
757 <param name="myrimatch_num_matches" type="integer" value="10"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
758 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
759 <param name="myrimatch_num_ptms" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
760 label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
761 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
762 <option value="CID" selected="True">CID</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
763 <option value="ETD" >ETD</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
764 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
765 <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
766 <option value="0">non-tryptic</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
767 <option value="1" >semi-tryptic</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
768 <option value="2" selected="True" >fully-tryptic</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
769 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
770 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
771 label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
772 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
773 label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
774 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
775 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
776 <param name="myrimatch_intensity_classes" type="integer" value="3"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
777 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
778 <param name="myrimatch_class_multiplier" type="integer" value="2"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
779 label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
780 <param name="myrimatch_num_batches" type="integer" value="50"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
781 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
782 <param name="myrimatch_max_peak" type="integer" value="100"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
783 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
784 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
785 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
786
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
787 <!-- Comet ADVANCED PARAMETERS -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
788 <conditional name="comet">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
789 <param name="comet_advanced" type="select" label="Comet Options">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
790 <option value="yes">Advanced</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
791 <option value="no" selected="True">Default</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
792 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
793 <when value="no" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
794 <when value="yes">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
795 <!-- Spectrum Related parameters -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
796 <conditional name="comet_spectrum">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
797 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
798 <option value="yes">Set Spectrum Parameters</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
799 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
800 </param>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
801 <when value="no" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
802 <when value="yes">
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
803 <param name="comet_min_peaks" type="integer" value="10"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
804 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
805 <param name="comet_min_peak_int" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
806 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
807 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
808 <option value="0" selected="True" >off</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
809 <option value="1">on</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
810 <option value="2">as expected for ETD/ECD spectra</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
811 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
812 <when value="0" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
813 <when value="1">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
814 <param name="comet_remove_prec_tol" type="float" value="1.5"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
815 label="Comet: Remove Precursor Tolerance" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
816 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
817 <when value="2">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
818 <param name="comet_remove_prec_tol" type="float" value="1.5"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
819 label="Comet: Remove Precursor Tolerance" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
820 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
821 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
822 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" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
823 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
824 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" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
825 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
826 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
827 <!-- Search Related parameters -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
828 <conditional name="comet_search">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
829 <param name="comet_search_selector" type="select" label="Comet: Search Related">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
830 <option value="yes">Set Search Parameters</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
831 <option value="no" selected="True">Keep Default Search Parameters</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
832 </param>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
833 <when value="no" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
834 <when value="yes">
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
835 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
836 <option value="1">semi-specific</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
837 <option value="2" selected="True">full-enzyme</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
838 <option value="8">unspecific N-term</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
839 <option value="9">unspecific C-term</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
840 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
841 <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">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
842 <option value="0" selected="True">off</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
843 <option value="1">-1,0,+1,+2,+3</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
844 <option value="2">-8,-4,0,+4,+8</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
845 </param>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
846 <param name="comet_min_prec_mass" type="float" value="0.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
847 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
848 <param name="comet_max_prec_mass" type="float" value="10000.0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
849 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
850 <param name="comet_num_matches" type="integer" value="10"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
851 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
852 <param name="comet_max_frag_charge" type="integer" value="3"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
853 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
854 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
855 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
856 <param name="comet_batch_size" type="integer" value="0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
857 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" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
858 <param name="comet_num_ptms" type="integer" value="10"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
859 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
860 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
861 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
862 <!-- Fragment Ions Related parameters -->
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
863 <conditional name="comet_fragment_ions">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
864 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
865 <option value="yes">Set Fragment Ions Parameters</option>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
866 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
867 </param>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
868 <when value="no" />
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
869 <when value="yes">
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
870 <param name="comet_frag_bin_offset" type="float" value="0.4"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
871 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
872 <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
873 label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
874 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
875 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
876 </when>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
877 </conditional>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
878
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
879 </when>
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
880 </conditional>
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
881 </inputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
882 <outputs>
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
883 <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
galaxyp
parents:
diff changeset
884 </outputs>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
885 <tests>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
886 <test>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
parents:
diff changeset
887 <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
galaxyp
parents:
diff changeset
888 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
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889 <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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890 <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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891 <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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892 <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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893 <param name="max_charge" value="3"/>
1
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894 <param name="XTANDEM_selector" value="True"/>
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895 <param name="xtandem.xtandem_advanced" value="yes"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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896 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
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897 <param name="OMSSA_selector" value="False"/>
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898 <param name="MSGF_selector" value="True"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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899 <param name="TIDE_selector" value="False"/>
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900 <param name="MYRIMATCH_selector" value="False"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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901 <param name="COMET_selector" value="False"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
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902 <param name="MS_AMANDA_selector" value="False"/>
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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903
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
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904 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" />
0
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905 </test>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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906 </tests>
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907 <help>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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908 **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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909
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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910 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
1
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911 Default: X! Tandem, OMSSA and MS-GF+ are executed.
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912 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
0
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913
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914
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915 </help>
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916 <expand macro="citations" />
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917 </tool>