Mercurial > repos > jjohnson > peptideshaker

annotate searchgui.xml @ 4:b4b1780ef40f draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit c624897f9f1282fe1708271a06554bf5a3465763-dirty
author jjohnson
date Thu, 12 Jul 2018 09:10:29 -0400
parents eea7e945f479
children
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
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2 <description>
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3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
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4 </description>
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5 <macros>
2
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6 <import>macros.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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10 <requirement type="package" version="3.0">zip</requirement>
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11 </requirements>
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12 <expand macro="stdio" />
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13 <command>
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14 <![CDATA[
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15 #from datetime import datetime
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16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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18 #set $temp_stderr = "searchgui_stderr"
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19 #set $bin_dir = "bin"
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21 mkdir output;
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22 mkdir output_reports;
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23 cwd=`pwd`;
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24 export HOME=\$cwd;
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26 ## echo the search engines to run
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27 echo "$search_engines_options.engines";
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28 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
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30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
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31 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
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33 #for $mgf in $peak_lists:
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34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
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35 ln -s -f '${mgf}' '${input_name}';
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36 #set $encoded_id = $__app__.security.encode_id($mgf.id)
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37 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
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38 #end for
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39 ##ln -s "${input_database}" input_database.fasta;
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40 cp "${input_database}" input_database.fasta;
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41
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42 ###########################################
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43 #### Creating decoy database ####
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44 ###########################################
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45 #if $protein_database_options.create_decoy:
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46 echo "Creating decoy database.";
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47 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
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48 rm input_database.fasta &&
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49 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
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50 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
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51 #end if
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52 @ENZYMESCLI@
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53 #####################################################
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54 ## generate IdentificationParameters for SearchGUI ##
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55 #####################################################
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56 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
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57 --exec_dir="\$cwd/${bin_dir}"
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58 -out SEARCHGUI_IdentificationParameters.par
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59
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60 @GENERAL_PARAMETERS@
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61
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62 -db input_database.fasta
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63 $protein_database_options.use_gene_mapping
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64 #if $protein_database_options.use_gene_mapping:
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65 $protein_database_options.update_gene_mapping
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66 #else:
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67 -updateGeneMapping 0
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68 #end if
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69
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70 #if $advanced_options.xtandem.xtandem_advanced == "yes"
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72 -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
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73 -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
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74 -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
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75 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
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76 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
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77 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
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78 -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
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79 -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
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80 -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
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81 -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
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82 -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
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83 -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
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84 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
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85 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
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86
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87 #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
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88 -xtandem_refine 1
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89 -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
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90 -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
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91 -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
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92 -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
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93 -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
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94 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
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95 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
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96
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97 #end if
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98 #else
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99 -xtandem_output_spectra 1
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100 #end if
0
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101
2
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102 #if $advanced_options.omssa.omssa_advanced == "yes"
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103 -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
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104 -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
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105 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
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106 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
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107 -omssa_memory ${advanced_options.omssa.omssa_memory}
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108 -omssa_neutron ${advanced_options.omssa.omssa_neutron}
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109 -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
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110 -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
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111 -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
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112 -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
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113 -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
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114 -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
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115 -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
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116 -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
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117 -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
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118 -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
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119 -omssa_methionine ${advanced_options.omssa.omssa_methionine}
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120 -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
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121 -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
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122 -omssa_fraction ${advanced_options.omssa.omssa_fraction}
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123 -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
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124 -omssa_charge ${advanced_options.omssa.omssa_charge}
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125 -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
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126 -omssa_forward ${advanced_options.omssa.omssa_forward}
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127 -omssa_rewind ${advanced_options.omssa.omssa_rewind}
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128 -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
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129 -omssa_corr ${advanced_options.omssa.omssa_corr}
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130 -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
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131 -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
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132 -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
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133 -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
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134 -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
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135 -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
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136 -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
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137 -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
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138 -omssa_format ${advanced_options.omssa.omssa_format}
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139 #end if
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140
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141 #if $advanced_options.msgf.msgf_advanced == "yes"
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142 -msgf_decoy ${advanced_options.msgf.msgf_decoy}
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143 -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
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144 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
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145 -msgf_termini ${advanced_options.msgf.msgf_termini}
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146 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
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147 -msgf_instrument ${advanced_options.msgf.msgf_instrument}
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148 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
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149 -msgf_protocol ${advanced_options.msgf.msgf_protocol}
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150 -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
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151 -msgf_additional ${advanced_options.msgf.msgf_additional}
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152 #end if
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153
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154 #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
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155 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
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156 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
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157 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
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158 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
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159 #end if
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160
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161 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
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162 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
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163 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
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164 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
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165 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
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166 -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
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167 -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
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168 -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
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169 -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
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170 -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
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171 -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
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172 -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
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173 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
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174 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
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175 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
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176 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
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177 #end if
0
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178
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179
2
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180 #* Not working in tests
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181 #if $advanced_options.andromeda.andromeda_advanced == "yes"
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182 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
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183 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
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184 -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
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185 -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
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186 -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
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187 -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
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188 -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
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189 -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
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190 -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
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191 -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
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192 -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
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193 -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
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194 -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
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195 -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
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196 -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
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197 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
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198 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
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199 #end if
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200 *#
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201
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202 #if $advanced_options.tide.tide_advanced == "yes"
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203 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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204 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
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205 #end if
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206 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
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207 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
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208 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
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209 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
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210 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
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211 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
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212 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
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213 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
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214 -tide_verbosity ${advanced_options.tide.tide_verbosity}
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215 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
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216 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
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217 -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
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218 -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
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219 -tide_max_psms ${advanced_options.tide.tide_max_psms}
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220 -tide_compute_p ${advanced_options.tide.tide_compute_p}
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221 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
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222 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
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223 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
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224 #end if
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225 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
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226 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
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227 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
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228 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
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229 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
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230 -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
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231 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
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232 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
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233 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
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234 -tide_concat ${advanced_options.tide.tide_concat}
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235
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236 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
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237 #for $format in $formats:
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238 #if str($advanced_options.tide.tide_export).strip() == $format:
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239 -$format 1
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240 #else:
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241 -$format 0
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242 #end if
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243
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244 #end for
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245
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246 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
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247
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248 #end if
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249
0
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250
2
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251 #if $advanced_options.comet.comet_advanced == "yes"
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252
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253 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
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254 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
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255 -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
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256
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257 -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
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258
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259
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260 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
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261 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
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262 #end if
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263
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264 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
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265 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
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266 #end if
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267
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268 -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
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269 -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
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270 #end if
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271
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272 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
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273 -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
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274 -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
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275 -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
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276 -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
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277 -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
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278 -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
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279 -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
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280 -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
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281 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
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282 #end if
0
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283
2
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284 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
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285 -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
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286 -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
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287 #end if
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288 #end if
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289
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290 #if $advanced_options.directtag.directtag_advanced == "yes"
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291 -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
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292 -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
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293 -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
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294 -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
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295 -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
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296 -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
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297 -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
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298 -directag_charge_states ${advanced_options.directtag.directag_charge_states}
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299 #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
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300 -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
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301 #end if
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302 -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
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303 -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
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304 -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
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305 -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
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306 -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
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307 -directag_tag_length ${advanced_options.directtag.directag_tag_length}
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308 -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
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309 -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
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310 -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
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311 -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
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312 -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
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313 #end if
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314
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315 #if $advanced_options.novor.novor_advanced == "yes"
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316 -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
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317 -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
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318 #end if
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319
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320 2> $temp_stderr)
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321 &&
0
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322
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323 ################
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324 ## Search CLI ##
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325 ################
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326 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
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327 --exec_dir="\$cwd/${bin_dir}"
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328 -temp_folder `pwd`
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329 -spectrum_files \$cwd
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330 -output_folder \$cwd/output
2
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331 @ENZYME_CONFIGUTRATION@
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332 -id_params SEARCHGUI_IdentificationParameters.par
0
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333
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334 -threads "\${GALAXY_SLOTS:-12}"
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335
2
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336 #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
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337 -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
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338 $advanced_options.searchgui_advanced.missing_titles
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339 -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
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340 -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}"
0
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341 #end if
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342
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343 ## 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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344 ## the tree is generated afterwards in PeptideShaker
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345 ## -protein_index 0
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346
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347 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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348
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349 #set $engines_list = str($search_engines_options.engines).split(',')
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350 #if 'X!Tandem' in $engines_list:
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351 -xtandem 1
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352 #else
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353 -xtandem 0
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354 #end if
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355
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356 #if 'MyriMatch' in $engines_list:
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357 -myrimatch 1
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358 #else
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359 -myrimatch 0
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360 #end if
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361
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362 #if 'MSGF' in $engines_list:
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363 -msgf 1
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364 #else
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365 -msgf 0
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366 #end if
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367
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368 #if 'OMSSA' in $engines_list:
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369 -omssa 1
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370 #else
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371 -omssa 0
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372 #end if
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373
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374 #if 'Comet' in $engines_list:
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375 -comet 1
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376 #else
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377 -comet 0
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378 #end if
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379
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380 #if 'Tide' in $engines_list:
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381 -tide 1
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382 #else
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383 -tide 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
384 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
385
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
386 #if 'MS_Amanda' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
387 -ms_amanda 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
388 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
389 -ms_amanda 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
390 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
391
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
392 #if 'Andromeda' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
393 -andromeda 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
394 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
395 -andromeda 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
396 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
397
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
398 #if 'Novor' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
399 -novor 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
400 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
401 -novor 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
402 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
403
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
404 #if 'DirecTag' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
405 -directag 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
406 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
407 -directag 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
408 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
409
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
410 ## single zip file
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
411 -output_option 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
412
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
413 ## mgf and database in output
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
414 -output_data 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
415
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
416 2>> $temp_stderr)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
417
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
418 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
419
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
420 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
421
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
422 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
423
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
424 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
425
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
426 exit_code_for_galaxy=\$?;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
427 cat $temp_stderr 2>&1;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
428 (exit \$exit_code_for_galaxy)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
429 ]]>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
430 </command>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
431 <inputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
432
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
433 <param format="fasta" name="input_database" type="data" label="Protein Database"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
434 help="Select FASTA database from history"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
435 <section name="protein_database_options" expanded="false" title="Protein Database Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
436 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
437 label="Create a concatenated target/decoy database before running PeptideShaker"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
438 help="Selecting this option will help PeptideShaker calculate FDR values" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
439 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
440 label="gene mappings will be used and saved along with the project (UniProt databases only)"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
441 help="This should only be enabled for UniProt databaases" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
442 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
443 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
444 help="This should only be enabled for UniProt databaases" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
445 </section>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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446 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
447 help="Select appropriate MGF dataset(s) from history" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
448
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
449 <!-- Search Engine Selection -->
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
450 <section name="search_engines_options" expanded="true" title="Search Engine Options">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
451 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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452 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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453 <option value="X!Tandem" selected="True">X!Tandem</option>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
454
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
455 <option value="MSGF" selected="True">MS-GF+</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
456 <option value="OMSSA" selected="True">OMSSA</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
457 <option value="Comet">Comet</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
458 <option value="Tide">Tide</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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459 <option value="MyriMatch">MyriMatch</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
460 <option value="MS_Amanda">MS_Amanda</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
461 <!-- Windows only
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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462 <option value="Andromeda">Andromeda</option>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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463 -->
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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464 <!-- New with version 3.0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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465 -->
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
466 <!--working in tests
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467 -->
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468 <option value="DirecTag">DirecTag</option>
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469 <option value="Novor">Novor (Select for non-commercial use only)</option>
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470 <validator type="no_options" message="Please select at least one output file" />
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471 </param>
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472 </section>
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473
2
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474
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475 <!-- General Parameters -->
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476 <expand macro="general_options"/>
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diff changeset
477
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diff changeset
478
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479 <section name="advanced_options" expanded="false" title="Andvanced Options">
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480 <!-- Optional Advanced SearchGUI Parameters -->
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481 <conditional name="searchgui_advanced">
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482 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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483 <option value="basic" selected="True">Default</option>
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484 <option value="advanced">Advanced</option>
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485 </param>
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486 <when value="basic" />
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487 <when value="advanced">
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488 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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489 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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490 <option value="0">no correction</option>
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491 <option value="1" selected="True">rename spectra</option>
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492 <option value="2">delete spectra</option>
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493 </param>
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494
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495 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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496 label="Add missing spectrum titles" help="(-missing_titles)"/>
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497
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498 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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499 help="Choose a smaller value if you are running on a machine with limited memory"/>
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500
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501 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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502 help="Choose a smaller value if you are running on a machine with limited memory"/>
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503 </when>
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504 </conditional>
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505
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506 <!-- X!TANDEM ADVANCED PARAMETERS -->
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507 <conditional name="xtandem">
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508 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
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509 <option value="yes">Advanced</option>
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510 <option value="no" selected="True">Default</option>
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511 </param>
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512 <when value="no" />
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513 <when value="yes">
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514 <param name="xtandem_npeaks" type="integer" value="50"
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515 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
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516 <param name="xtandem_min_peaks" type="integer" value="15"
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517 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
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518 <param name="xtandem_min_frag_mz" type="integer" value="200"
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519 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
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520 <param name="xtandem_min_prec_mass" type="integer" value="200"
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521 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
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522 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
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523 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
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524 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
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525 label="X!Tandem: Dynamic Range" value="100" type="integer" />
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526 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
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527 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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528 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
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529 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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530 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
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531 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
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532 <param name="xtandem_evalue" help="Highest value for recorded peptides"
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533 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
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534 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
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535 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
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536 <param name="xtandem_output_sequences" help="Controls output of sequence information"
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537 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
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538 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
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539 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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540 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
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541
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542 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
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543 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
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544 <option value="no" selected="True">Don't refine</option>
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545 <option value="yes" >Use refinement</option>
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546 </param>
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547 <when value="no"/>
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548 <when value="yes">
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549 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
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550 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
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551 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
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552 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
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553 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
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554 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
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555 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
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556 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
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557 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
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558 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
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559 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
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560 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
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561 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
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562 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
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563 </when>
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564 </conditional>
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565 </when>
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566 </conditional>
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567
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568 <!-- OMSSA ADVANCED PARAMETERS -->
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569 <conditional name="omssa">
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570 <param name="omssa_advanced" type="select" label="OMSSA Options">
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571 <option value="yes">Advanced</option>
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572 <option value="no" selected="True">Default</option>
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573 </param>
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574 <when value="no" />
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575 <when value="yes">
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576 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
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577 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
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578 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
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579 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
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580
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581 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
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582 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
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583 <param name="omssa_neutron" type="float" value="1446.94"
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584 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
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585 <param name="omssa_low_intensity" type="float" value="0.0"
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586 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
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587 <param name="omssa_high_intensity" type="float" value="0.2"
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588 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
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589 <param name="omssa_intensity_incr" type="float" value="0.0005"
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590 label="OMSSA: Intensity Increment" help="Intensity increment" />
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591 <param name="omssa_single_window_wd" type="integer" value="27"
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592 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
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593 <param name="omssa_double_window_wd" type="integer" value="14"
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594 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
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595 <param name="omssa_single_window_pk" type="integer" value="2"
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596 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
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597 <param name="omssa_double_window_pk" type="integer" value="2"
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598 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
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599 <param name="omssa_min_ann_int_pks" type="integer" value="6"
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600 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
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601 <param name="omssa_min_annotated_peaks" type="integer" value="2"
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602 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
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603 <param name="omssa_min_peaks" type="integer" value="4"
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604 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
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605 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
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606 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
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607 <param name="omssa_max_ladders" type="integer" value="128"
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608 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
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609 <param name="omssa_max_frag_charge" type="integer" value="2"
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610 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
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611 <param name="omssa_fraction" type="float" value="0.95"
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612 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
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613 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
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614 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
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615 <param name="omssa_charge" type="select"
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616 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
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617 <option value="0" >Minus</option>
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618 <option value="1" selected="True">Plus</option>
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parents: 1
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619 </param>
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620 <param name="omssa_prec_per_spectrum" type="integer" value="1"
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parents: 1
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621 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
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parents: 1
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622 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
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parents: 1
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623 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
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parents: 1
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624 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
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jjohnson
parents: 1
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625 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
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parents: 1
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626 <param name="omssa_max_frag_series" type="integer" value="100"
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jjohnson
parents: 1
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627 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
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628 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
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parents: 1
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629 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
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630 <param name="omssa_consecutive_p" type="float" value="0.5"
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631 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
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632 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
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633 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
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634 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
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635 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
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636 <param name="omssa_it_replace_evalue" type="float" value="0.01"
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637 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
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638 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
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639 label="OMSSA: Remove Precursor" help="Remove precursors" />
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640 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
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641 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
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642 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
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643 label="OMSSA: Remove Precursor" help="Remove precursors" />
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644 <param name="omssa_max_evalue" type="float" value="100"
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645 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
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646 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
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647 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
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648 <param name="omssa_it_replace_evalue" type="float" value="100"
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649 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
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650 <param name="omssa_hitlist_length" type="integer" value="0"
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651 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
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652 <param name="omssa_hitlist_charge" type="integer" value="30"
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653 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
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654 <param name="omssa_min_pep_length" type="integer" value="4"
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655 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
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656 <param name="omssa_max_pep_length" type="integer" value="40"
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657 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
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658 <param name="omssa_format" label="OMSSA output format" type="select" >
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659 <option value="0" selected="True">OMX</option>
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660 <option value="1" >CSV</option>
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661 </param>
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662 </when>
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663 </conditional>
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664
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665 <!-- MS-GF+ ADVANCED PARAMETERS -->
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666 <conditional name="msgf">
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667 <param name="msgf_advanced" type="select" label="MSGF Options">
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668 <option value="yes">Advanced</option>
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669 <option value="no" selected="True">Default</option>
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670 </param>
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671 <when value="no" />
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672 <when value="yes">
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673 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
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674 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
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675 <param name="msgf_min_pep_length" type="integer" value="6"
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676 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
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677 <param name="msgf_max_pep_length" type="integer" value="30"
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678 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
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679 <param name="msgf_termini" type="select" format="txt"
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680 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
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681 <option value="0">0 (ie non-specific cleavage)</option>
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682 <option value="1">1 (ie semi-tryptic cleavage)</option>
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683 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
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684 </param>
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685 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
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686
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687 <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)">
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688 <option value="0" selected="True">Low-res LCQ/LTQ</option>
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689 <option value="1" >High-res LTQ</option>
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690 <option value="2" >TOF</option>
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691 <option value="3" >Q-Exactive</option>
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692 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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693 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
694 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
695 <option value="1" >CID</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
696 <option value="2" >ETD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
697 <option value="3" >HCD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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698 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
699 <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">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
700 <option value="0" selected="True">Automatic</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
701 <option value="1" >Phosphorylation</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
702 <option value="2" >iTRAQ</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
703 <option value="3" >iTRAQPhospho</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
704 <option value="4" >TMT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
705 <option value="5" >Standard</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
706 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
707 <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" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
708 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
709 <option value="0" selected="True">output basic scores only</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
710 <option value="1" >output additional features</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
711 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
712 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
713 </conditional>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
714
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
715 <!-- MS-AMANDA ADVANCED PARAMETERS -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
716 <conditional name="ms_amanda">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
717 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
718 <option value="yes">Advanced</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
719 <option value="no" selected="True">Default</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
720 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
721 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
722 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
723 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
724 label="MS Amanda: Generate Decoys" help="generate decoys" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
725 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
726 help="MS Amanda instrument id option. Available ion types are listed here.">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
727
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
728 <option value="b, y" selected="True">b, y</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
729 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
730 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
731 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
732 <option value="a, b, y" >a, b, y</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
733 <option value="a, b, y, Imm" >a, b, y, Imm</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
734 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
735 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
736 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
737 <option value="b, y, INT" >b, y, INT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
738 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
739 <option value="a, b, y, INT" >a, b, y, INT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
740 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
741 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
742 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
743 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
744
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
745 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
746 <param name="ms_amanda_max_rank" type="integer" value="10"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
747 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
748 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
749 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
750 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
751 </conditional>
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jjohnson
parents: 1
diff changeset
752
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
753
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
754 <!-- TIDE ADVANCED PARAMETERS -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
755 <conditional name="tide">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
756 <param name="tide_advanced" type="select" label="TIDE Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
757 <option value="yes">Advanced</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
758 <option value="no" selected="True">Default</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
759 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
760 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
761 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
762 <param name="tide_num_ptms" type="integer" value="" optional="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
763 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
764 <param name="tide_num_ptms_per_type" type="integer" value="2"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
765 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
766 <param name="tide_min_pep_length" type="integer" value="6"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
767 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
768 <param name="tide_max_pep_length" type="integer" value="30"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
769 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
770 <param name="tide_min_prec_mass" type="float" value="200.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
771 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
772 <param name="tide_max_prec_mass" type="float" value="7200.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
773 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
774 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
775 <option value="none" selected="True">none</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
776 <option value="shuffle" >shuffle</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
777 <option value="peptide-revers" >peptide-reverse</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
778 <option value="protein-reverse" >protein-reverse</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
779 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
780 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
781 <option value="N" >N</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
782 <option value="C" >C</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
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783 <option value="NC" selected="True">NC</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
784 <option value="non" >none</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
785 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
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786 <param name="tide_decoy_seed" type="integer" value="1"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
787 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
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788 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
789 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
790 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
791 <option value="0" >0</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
792 <option value="10" >10</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
793 <option value="20" >20</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
794 <option value="30" selected="True">30</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
795 <option value="40" >40</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
796 <option value="50" >50</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
797 <option value="60" >60</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
798 </param>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
799
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
800 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
801 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
802 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
803 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
804 <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">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
805 <option value="full-digest" selected="True">full-digest</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
806 <option value="partial-digest" >partial-digest</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
807 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
808 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
809 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
810 <param name="tide_max_psms" type="integer" value="10"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
811 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
812 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
813 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
814 <param name="tide_min_spectrum_mz" type="float" value="0.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
815 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
816 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
817 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
818 <param name="tide_min_spectrum_peaks" type="integer" value="20"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
819 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
820 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
821 <option value="1" >1</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
822 <option value="2" >2</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
823 <option value="3" >3</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
824 <option value="all" selected="True">all</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
825 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
826 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
827 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
828 <param name="tide_remove_prec_tol" type="float" value="1.5"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
829 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
830 <param name="tide_progress_indicator" type="integer" value="1000"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
831 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
832 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
833 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
834 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
835 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
836 <param name="tide_mz_bin_width" type="float" value="0.02"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
837 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
838 <param name="tide_mz_bin_offset" type="float" value="0.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
839 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
840 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
841 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
842
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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843 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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844 <option value="tide_export_text" selected="True">Text</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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845 <option value="tide_export_sqt" >SQT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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846 <option value="tide_export_pepxml" >pepxml</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
847 <option value="tide_export_mzid" >MzIdentML</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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848 <option value="tide_export_pin" >Percolator input file</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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849 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
850
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
851 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
852 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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853 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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854 </conditional>
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parents: 1
diff changeset
855
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
856
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
857 <!-- MyriMatch ADVANCED PARAMETERS -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
858 <conditional name="myrimatch">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
859 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
860 <option value="yes">Advanced</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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861 <option value="no" selected="True">Default</option>
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862 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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863 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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864 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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865 <param name="myrimatch_min_pep_length" type="integer" value="8"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
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866 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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867 <param name="myrimatch_max_pep_length" type="integer" value="30"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
868 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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869 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
870 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
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871 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
872 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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873 <param name="myrimatch_num_matches" type="integer" value="10"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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874 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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875 <param name="myrimatch_num_ptms" type="integer" value="2"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
876 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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877 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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878 <option value="CID" selected="True">CID</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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879 <option value="HCD" >HCD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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880 <option value="ETD" >ETD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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881 </param>
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parents: 1
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882 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
883 <option value="0">None required</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
884 <option value="1">At least one</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
885 <option value="2" selected="True" >Both</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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886 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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887 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
888 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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889 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
890 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
891 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
892 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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893 <param name="myrimatch_intensity_classes" type="integer" value="3"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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894 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
895 <param name="myrimatch_class_multiplier" type="integer" value="2"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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896 label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
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897 <param name="myrimatch_num_batches" type="integer" value="50"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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898 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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899 <param name="myrimatch_max_peak" type="integer" value="100"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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900 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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901 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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902 </conditional>
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903
0
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parents:
diff changeset
904
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
905 <!-- Andromeda ADVANCED PARAMETERS -->
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diff changeset
906 <!-- Windows only
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907 <conditional name="andromeda">
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908 <param name="andromeda_advanced" type="select" label="Andromeda Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
909 <option value="yes">Advanced</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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910 <option value="no" selected="True">Default</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
911 </param>
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parents: 1
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912 <when value="no" />
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913 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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914 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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915 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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916 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
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917 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
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918 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
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parents: 1
diff changeset
919 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
920 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
921 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
922 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
923 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
924 <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
925 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
926 <option value="CID" selected="true">CID</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
927 <option value="HCD">HCD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
928 <option value="EDT">EDT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
929 </param>
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jjohnson
parents: 1
diff changeset
930 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
931 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
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jjohnson
parents: 1
diff changeset
932 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
933 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
934 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
935 </when>
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parents: 1
diff changeset
936 </conditional>
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jjohnson
parents: 1
diff changeset
937 -->
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
938
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
939 <!-- Comet ADVANCED PARAMETERS -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
940 <conditional name="comet">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
941 <param name="comet_advanced" type="select" label="Comet Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
942 <option value="yes">Advanced</option>
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parents: 1
diff changeset
943 <option value="no" selected="True">Default</option>
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parents: 1
diff changeset
944 </param>
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parents: 1
diff changeset
945 <when value="no" />
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jjohnson
parents: 1
diff changeset
946 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
947 <!-- Spectrum Related parameters -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
948 <conditional name="comet_spectrum">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
949 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
950 <option value="yes">Set Spectrum Parameters</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
951 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
952 </param>
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jjohnson
parents: 1
diff changeset
953 <when value="no" />
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jjohnson
parents: 1
diff changeset
954 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
955 <param name="comet_min_peaks" type="integer" value="10"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
956 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
957 <param name="comet_min_peak_int" type="float" value="0.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
958 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
959 <conditional name="comet_prec">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
960 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
961 <option value="0" selected="True" >off</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
962 <option value="1">on</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
963 <option value="2">as expected for ETD/ECD spectra</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
964 </param>
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jjohnson
parents: 1
diff changeset
965 <when value="0" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
966 <when value="1">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
967 <param name="comet_remove_prec_tol" type="float" value="1.5"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
968 label="Comet: Remove Precursor Tolerance" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
969 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
970 <when value="2">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
971 <param name="comet_remove_prec_tol" type="float" value="1.5"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
972 label="Comet: Remove Precursor Tolerance" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
973 </when>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
974 </conditional>
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parents: 1
diff changeset
975 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
976 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" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
977 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
978 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" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
979 </when>
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parents: 1
diff changeset
980 </conditional>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
981 <!-- Search Related parameters -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
982 <conditional name="comet_search">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
983 <param name="comet_search_selector" type="select" label="Comet: Search Related">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
984 <option value="yes">Set Search Parameters</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
985 <option value="no" selected="True">Keep Default Search Parameters</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
986 </param>
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jjohnson
parents: 1
diff changeset
987 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
988 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
989 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
990 <option value="1">semi-specific</option>
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parents: 1
diff changeset
991 <option value="2" selected="True">full-enzyme</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
992 <option value="8">unspecific N-term</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
993 <option value="9">unspecific C-term</option>
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994 </param>
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995 <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">
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996 <option value="0" selected="True">off</option>
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997 <option value="1">-1,0,+1,+2,+3</option>
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998 <option value="2">-8,-4,0,+4,+8</option>
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999 </param>
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1000 <param name="comet_min_prec_mass" type="float" value="0.0"
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1001 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
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1002 <param name="comet_max_prec_mass" type="float" value="10000.0"
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1003 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
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1004 <param name="comet_num_matches" type="integer" value="10"
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1005 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
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1006 <param name="comet_max_frag_charge" type="integer" value="3"
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parents: 1
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1007 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
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1008 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
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parents: 1
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1009 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
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parents: 1
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1010 <param name="comet_batch_size" type="integer" value="0"
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1011 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" />
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1012 <param name="comet_num_ptms" type="integer" value="10"
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1013 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
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1014 </when>
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parents: 1
diff changeset
1015 </conditional>
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parents: 1
diff changeset
1016 <!-- Fragment Ions Related parameters -->
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parents: 1
diff changeset
1017 <conditional name="comet_fragment_ions">
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1018 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
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1019 <option value="yes">Set Fragment Ions Parameters</option>
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diff changeset
1020 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
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1021 </param>
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diff changeset
1022 <when value="no" />
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parents: 1
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1023 <when value="yes">
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1024 <param name="comet_frag_bin_offset" type="float" value="0.4"
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1025 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
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1026 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
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1027 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
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1028 </when>
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1029 </conditional>
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parents: 1
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1030 </when>
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1031 </conditional>
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1032 <conditional name="directtag">
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1033 <param name="directtag_advanced" type="select" label="DirectTag Options">
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1034 <option value="yes">Advanced</option>
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1035 <option value="no" selected="True">Default</option>
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1036 </param>
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1037 <when value="no" />
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1038 <when value="yes">
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1039 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
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1040 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
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1041 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
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1042 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
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1043 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
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1044 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
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1045 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
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1046 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
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1047 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
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1048 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
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1049 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
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1050 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
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1051 <option value="0" selected="true">no deisotoping</option>
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1052 <option value="1">precursor only</option>
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1053 <option value="2">precursor and candidate</option>
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1054 </param>
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1055 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
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1056 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
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1057 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
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1058 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
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1059 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
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1060 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
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1061 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
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1062 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
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1063 </when>
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1064 </conditional>
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1065
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diff changeset
1066 <conditional name="novor">
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jjohnson
parents: 1
diff changeset
1067 <param name="novor_advanced" type="select" label="Novor Options">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1068 <option value="yes">Advanced</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1069 <option value="no" selected="True">Default</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1070 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1071 <when value="no" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1072 <when value="yes">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1073 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1074 <option value="HCD" selected="True">HCD</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1075 <option value="CID">CID</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1076 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1077 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1078 <option value="FT" selected="True">FT</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1079 <option value="Trap" >Trap</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1080 <option value="TOF" >TOF</option>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1081 </param>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1082 </when>
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jjohnson
parents: 1
diff changeset
1083 </conditional>
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jjohnson
parents: 1
diff changeset
1084 </section>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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diff changeset
1085 </inputs>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
1086 <outputs>
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diff changeset
1087 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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diff changeset
1088 </outputs>
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jjohnson
parents:
diff changeset
1089 <tests>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
1090
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
1091 <!-- Test that specifying non-default search engines works -->
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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diff changeset
1092 <test>
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diff changeset
1093 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1094 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
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diff changeset
1095 <param name="precursor_ion_tol" value="100"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1096 <param name="min_charge" value="1"/>
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jjohnson
parents: 1
diff changeset
1097 <param name="max_charge" value="3"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
1098 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1099 <param name="xtandem.xtandem_advanced" value="yes"/>
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diff changeset
1100 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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parents: 0
diff changeset
1101 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
0
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diff changeset
1102 </test>
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parents:
diff changeset
1103 <!-- Test that search works with MSAmanda -->
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diff changeset
1104 <test>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1105 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1107 <param name="precursor_ion_tol" value="100"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1108 <param name="min_charge" value="1"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1109 <param name="max_charge" value="3"/>
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
1110 <param name="engines" value="MS_Amanda"/>
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1111 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
1112 </test>
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1113
2
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1114 <!-- Test that specifying non-default search engines works using modifications -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
jjohnson
parents: 1
diff changeset
1115 <!--
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1116 <test>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1118 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1119 <param name="precursor_ion_tol" value="100"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1120 <param name="fixed_modifications" value="carbamidomethyl c"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1121 <param name="variable_modifications" value="oxidation of m"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1122 <param name="min_charge" value="1"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1123 <param name="max_charge" value="3"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1124 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1125 <param name="xtandem.xtandem_advanced" value="yes"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1126 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1127 <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1128 </test>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1129 -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1130 <!-- Test that search works with MSAmanda - with modifications -->
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1131 <!--
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1132 <test>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1133 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1134 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1135 <param name="precursor_ion_tol" value="100"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1136 <param name="fixed_modifications" value="carbamidomethyl c"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1137 <param name="variable_modifications" value="oxidation of m"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1138 <param name="min_charge" value="1"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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parents: 1
diff changeset
1139 <param name="max_charge" value="3"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1140 <param name="engines" value="MS_Amanda"/>
eea7e945f479 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
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diff changeset
1141 <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
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diff changeset
1142 </test>
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diff changeset
1143 -->
0
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1144 </tests>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1145 <help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1146 **What it does**
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1147
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1148 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1149 Default: X! Tandem, OMSSA and MS-GF+ are executed.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1150 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1151
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1152 </help>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1153 <expand macro="citations" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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1154 </tool>