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annotate macros.xml @ 6:59fec1e2a6c3 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
author galaxyp
date Sun, 30 Mar 2025 23:00:45 +0000
parents e06c94fe89cc
children
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41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1 <macros>
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2 <import>msfragger_macros.xml</import>
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3 <token name="@TOOL_VERSION@">20.0</token>
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4 <token name="@VERSION_SUFFIX@">6</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
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8 </requirements>
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9 </xml>
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11 <!-- TMT-n uses the following n first labels from TMT-18 -->
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12 <token name="@TMT_LABELS@">['126', '127N', '127C', '128N', '128C', '129N', '129C', '130N', '130C', '131N', '131C', '132N', '132C', '133N', '133C', '134N', '134C', '135N']</token>
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13 <token name="@iTRAQ-4_LABELS@">['114', '115', '116', '117']</token>
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14 <token name="@iTRAQ-8_LABELS@">['113', '114', '115', '116', '117', '118', '119', '121']</token>
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16 <!--
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17 User specifies input file format and selects sample files as are included by the scan_inputs macro
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19 User must also supply their own manifest file, a TSV file of the format:
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20 name, experiment, bioreplicate, data type
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21 -->
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22 <xml name="samples">
2
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23 <param name="inputs" type="data" format="mzml,mzxml,thermo.raw" multiple="true" label="Proteomics Spectrum files" help="All input scan files must be named with one of the following extensions: .mzML, .mzXML, or .raw"/>
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24 <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
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25 <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
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26 </param>
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27 <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be .mzML, .mzXML, or .raw.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
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28 </xml>
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30 <!--
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31 Prepares enviroment variables for FragPipe.
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32 -->
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33 <token name="@PREPARE_ENVIRONMENT@"><![CDATA[
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34 env_location="\$(dirname \$(which philosopher))/.." &&
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35 cp -r \${env_location}/share/fragpipe*/ fragpipe_local/ &&
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36 mkdir .cache .config tmp &&
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37 export XDG_CONFIG_HOME=\$(pwd)/.config &&
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38 export XDG_CACHE_HOME=\$(pwd)/.cache &&
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39 export JAVA_OPTS="\$JAVA_OPTS -Djava.io.tmpdir=\$(pwd)/tmp" &&
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40 export LD_LIBRARY_PATH="\$LD_LIBRARY_PATH:/usr/local/lib" &&
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41 ]]></token>
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43 <!--
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44 Prepares input scan files.
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45
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46 Scans and moved to a scan directory and linked.
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47
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48 Annotation files are copied into the scan directory for TMT workflows.
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49 -->
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50 <token name="@LINK_SAMPLES@"><![CDATA[
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51 CWD=\$(pwd | sed 's@/@\\/@g') &&
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52
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53 mkdir -p scans &&
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54 #if $wf.workflow_name == "TMT10" or $wf.workflow_name == "TMT11"
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55 cp -p '$wf.annotation' 'scans/annotation.txt' &&
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56 #end if
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58 sed "s@^@\$CWD/scans/@" $manifest > fp.manifest &&
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59
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60 #for $sf in $inputs
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61 #set $i_name = $ln_name($sf)
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62 ln -s '$sf' 'scans/${i_name}' &&
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63 #end for
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64 ]]></token>
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65
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66 <!--
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67 Prepares input files, excluding database.
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68 -->
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69 <token name="@PREPARE_INPUTS@"><![CDATA[
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70 mkdir -p outputs &&
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71 @CMD_IMPORTS@
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72 @LINK_SAMPLES@
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73 ]]></token>
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74
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75 <!--
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76 Prepares database.
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77
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78 First genericizes unknown sequence headers in the database.
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79 Then adds decoys, or decoys and contaminants depending on user selection.
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80 -->
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81 <token name="@PREPARE_DATABASE@"><![CDATA[
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82 '$__tool_directory__/genericize_db.py' $database_name genericized_db.fas &&
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83
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84 #if str($database_options) != 'none'
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85 philosopher workspace --init &&
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86 philosopher database --custom genericized_db.fas --prefix rev_
6
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87 #if str($database_options) == 'decoy_and_contam'
0
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88 --contam
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89 #end if
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90 --contamprefix &&
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91 ln -s *-decoys-*.fas final_db.fas &&
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92 #else
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93 ln -s genericized_db.fas final_db.fas &&
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94 #end if
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95 ]]></token>
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96
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97 <!--
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98 Prepares outputs.
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99
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100 Creates log file symlink, makes a new directory for "combined" outputs and creates "concatenated" results.
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101 -->
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102 <token name="@PREPARE_OUTPUTS@"><![CDATA[
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103 cd outputs &&
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104
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105 #if $output_options and 'combined_outputs' in $output_options
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106 mkdir combined_outputs &&
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107 find . -name 'combined*tsv' | xargs -I {} mv {} combined_outputs &&
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108 #end if
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109
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110 ## For each category of results - psm, ion, peptide, protein - this loop concatenates results from each sample into a single result.
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111 ## For example, the entries sample1/psm.tsv and sample2/psm.tsv would be combined to concat_psm.tsv, a single psm.tsv header as its first line.
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112 for f in psm.tsv ion.tsv peptide.tsv protein.tsv; do
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113 n=0;
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114 for i in \$(find * -name \${f}); do
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115 d=\${i%/*};
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116 if [[ \$n == 0 ]]; then
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117 awk 'NR==1{printf("Experiment\t%s\n",\$0);}' \$i > concat_\${f};
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118 fi;
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119 awk 'NR>1{printf("'"\${d}"'\t%s\n",\$0);}' \$i >> concat_\${f}; t=\$(echo \${i} | tr '/' '.');
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120 mv \${i} \${t}; n=\$((n+1));
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121 done;
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122 done
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123 ]]></token>
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124
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125 <!-- Input database for MSFragger -->
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126 <xml name="fragger_database">
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127 <param name="database_name" type="data" format="fasta" label="Proteomics Search Database in FASTA format" help="Generic sequence headers in the input FASTA file that are not formatted according to the UniProt, NCBI, or ENSEMBL formats will be automatically prefixed with '>generic|' to avoid being misinterpreted by Philosopher."/>
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128 <!-- Whether to add decoys and contaminants to the database with Philosopher -->
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129 <param name="database_options"
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130 type="select"
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131 label="Decoys and contaminants"
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132 help="The default decoy prefix is &quot;rev_&quot;.">
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133 <option value="decoy_and_contam" selected="true">Add decoys and contaminants</option>
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134 <option value="decoy">Add decoys</option>
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135 <option value="none">Don't add decoys or contaminants</option>
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136 </param>
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137
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138 <!-- Database may be split into chunks for performance benefits -->
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139 <param name="num_slices" type="integer" label="Split database" value="1" help="The number of chunks in which to split the database."/>
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140 </xml>
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141
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142 <!--
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143 The following macro allows users to select their FragPipe workfow.
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144
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145 For a given workflow selection, the relevant parameter sections are expanded. Options specific to the selected workflow
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146 are passed to the parameter definitions in the expand element.
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147
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148 The Galaxy parameters overwrite a workflow file provided by FragPipe for the selected workflow. As a result, any parameters
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149 that are not defined in the Galaxy tool will fall back on the FragPipe defaults for that workflow. This logic is defined
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150 in the <configfile> element.
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151 -->
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152 <xml name="workflow">
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153 <conditional name="wf">
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154 <param name="workflow_name" type="select" label="Workflow" help="Note: MSBooster is currently disabled in all Galaxy FragPipe workflows.">
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155 <option value="Default">Default</option>
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156 <option value="Open">Open</option>
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157 <option value="Nonspecific-HLA">Nonspecific-HLA</option>
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158 <option value="LFQ-MBR">LFQ-MBR</option>
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159 <option value="TMT10">TMT10</option>
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160 <option value="TMT11">TMT11</option>
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161 </param>
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162
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163 <when value="Default">
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164 <section name="msfragger" expanded="false" title="MSFragger Options">
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165 <expand macro="msfragger_default"/>
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166 </section>
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167 <expand macro="validation"
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168 pep="false"
6
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169 perc="false"
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170 boost="true"
0
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171 no="false"
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172 masswidth="5"
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diff changeset
173 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
174 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
175 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
176 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
177 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
178 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
179 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
180 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
181 <expand macro="ptm_shepherd" yes="false" no="true" c="true" z="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
182 <expand macro="isobaric_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
183 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
184
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
185 <when value="Open">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
186 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
187 <expand macro="msfragger_open"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
188 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
189 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
190 pep="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
191 perc="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
192 boost="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
193 no="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
194 masswidth="1000"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
195 clevel="-2"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
196 accmass="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
197 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
198 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
199 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
200 ppm="false"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
201 combined_pepxml="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
202 <expand macro="crystalc"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
203 </expand>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
204 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
205 <expand macro="ptm_shepherd" yes="true" no="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
206 <expand macro="isobaric_quantification" yes="false" no="true" bridge="false" pool="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
207 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
208
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
209 <when value="Nonspecific-HLA">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
210 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
211 <expand macro="msfragger_nonspecific_HLA"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
212 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
213 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
214 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
215 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
216 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
217 no="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
218 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
219 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
220 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
221 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
222 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
223 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
224 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
225 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
226 <expand macro="label_free_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
227 <expand macro="ptm_shepherd" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
228 <expand macro="isobaric_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
229 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
230
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
231 <when value="LFQ-MBR">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
232 <section name="msfragger" expanded="false" title="MSFragger Options">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
233 <expand macro="msfragger_LFQ_MBR"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
234 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
235 <expand macro="validation"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
236 pep="false"
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
237 perc="false"
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
238 boost="true"
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
239 no="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
240 masswidth="5"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
241 clevel="0"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
242 accmass="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
243 decoyprobs="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
244 nonparam="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
245 expectscore="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
246 ppm="true"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
247 combined_pepxml="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
248 <expand macro="label_free_quantification" yes="true" no="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
249 <expand macro="ptm_shepherd" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
250 <expand macro="isobaric_quantification" yes="false" no="true"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
251 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
252
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
253 <when value="TMT10">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
254 <expand macro="tmt_options" plex="TMT-10"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
255 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
256
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
257 <!-- TMT11 is not in FragPipe GUI -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
258 <when value="TMT11">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
259 <expand macro="tmt_options" plex="TMT-11"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
260 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
261 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
262 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
263
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
264 <!-- Options for TMT workflows -->
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265 <xml name="tmt_options" token_plex="">
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266 <param name="annotation" type="data" format="txt" optional="false" label="annotation file" help=""/>
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267 <section name="msfragger" expanded="false" title="MSFragger Options">
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268 <expand macro="msfragger_TMT"/>
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269 </section>
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270 <expand macro="validation"
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271 pep="false"
6
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272 perc="false"
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273 boost="true"
0
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274 no="false"
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275 masswidth="5"
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276 clevel="0"
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277 accmass="true"
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278 decoyprobs="true"
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279 nonparam="true"
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280 expectscore="true"
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281 ppm="true"
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282 combined_pepxml="false"
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283 protp_minprob="0.5"/>
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284 <expand macro="isobaric_quantification" yes="true" no="false" plex="@PLEX@" level="2" ref_tag="Bridge" mod_tag="none"/>
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285 <expand macro="label_free_quantification" yes="false" no="true"/>
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286 <expand macro="ptm_shepherd" yes="false" no="true" token_unimod="false" token_common="true"/>
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287 </xml>
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288
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289 <!-- Generates the FragPipe workflow-->
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290 <xml name="workflow_configfile">
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291 <configfile name="workflow_configfile"><![CDATA[#slurp
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292 ## Create a fragpipe params dictionary from a file
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293 #set $comments = []
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294 #set $wfdict = {}
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295 #set $wfpath = $__tool_directory__ + '/workflows/' + str($wf.workflow_name) + '.workflow'
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296 #set $fh = open($wfpath, 'r')
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297 #for $line in $fh:
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298 #if $line.startswith('#')
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299 #silent $comments.append($line)
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300 #elif $line.strip() != ''
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301 #set $kv = $line.strip().split('=')
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302 #if len($kv) < 2
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303 #silent $kv.append('')
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304 #end if
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305 #set $wfdict[$kv[0]] = '='.join($kv[1:])
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306 #end if
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307 #end for
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308
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309 #set $wfdict['database.db-path'] = 'final_db.fas'
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310 #set $wfdict['msfragger.misc.slice-db'] = $num_slices
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311
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312 ## Get the MSFragger Params (shared with the MSFragger tool)
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313 #set $prefix = $wf.msfragger
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314 @MSFRAGGER_PARAM_DICT@
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315 #if len($vmods) > 0
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316 #set $msfragger_dict['table.var-mods'] = '; '.join([$re.sub('^(.*,)(\d)$','\\1True,\\2',m) for m in $vmods])
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317 #end if
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318 #for $k in $msfragger_dict.keys()
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319 #set $kv = $k + '=' + str($msfragger_dict[$k])
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320 #set $wfk = 'msfragger.' + $k
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321 #set $wfdict[$wfk] = str($msfragger_dict[$k])
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322 #end for
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323
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324 @VALIDATION@
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325 @PTM_SHEPHERD@
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326 @LABEL_FREE_QUANTIFICATION@
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327 @ISOBARIC_QUANTIFICATION@
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328
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329 ## Populate the workflow with configuration and comment dictionary entries populated by tool params.
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330 #for $comment in $comments
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331 $comment
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332 #end for
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333
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334 #for $k in sorted($wfdict.keys())
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335 #set $kv = $k + '=' + str($wfdict[$k])
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336 $kv
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337 #end for
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338 #slurp]]></configfile>
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339 </xml>
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340
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341 <!-- Percolator options -->
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342 <xml name="percolator">
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343 <section name="percolator" expanded="true" title="Percolator">
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344 <param name="keep_tsv_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Keep intermediate files"/>
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345 <param name="min_prob" type="float" value="0.5" label="Minimum probability (default 0.5)"/>
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346 </section>
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347 </xml>
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348
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349 <!-- Set Percolator workflow options -->
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350 <token name="@PERCOLATOR@"><![CDATA[
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351 #set $prc = $wf.validation.validation_tab.psm_validation.percolator
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352 #set $wfdict['percolator.run-percolator'] = 'true'
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353 #set $wfdict['percolator.keep-tsv-files'] = str($prc.keep_tsv_files)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
354 #set $wfdict['percolator.min-prob'] = str($prc.min_prob)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
355 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
356
4
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
357 <xml name="msbooster">
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
358 <section name="msbooster" expanded="true" title="MSBooster">
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
359 <param name="predict_rt" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict RT"/>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
360 <param name="predict_spectra" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Predict spectra"/>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
361 <param name="use_correlated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use correlated features"/>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
362 </section>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
363 </xml>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
364 <token name="@MSBOOSTER@"><![CDATA[
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
365 #set $prfx = $wf.validation.validation_tab.psm_validation.msbooster
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
366 #set $wfdict['msbooster.run-msbooster'] = 'true'
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
367 #set $wfdict['msbooster.predict-rt'] = str($prfx.predict_rt)
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
368 #set $wfdict['msbooster.predict-spectra'] = str($prfx.predict_spectra)
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
369 #set $wfdict['msbooster.use-correlated-features'] = str($prfx.use_correlated_features)
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
370 ]]></token>
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
371
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
372
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
373 <!-- Philosopher Report (phi-report) options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
374 <xml name="phi_report">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
375 <conditional name="phi_report">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
376 <param name="run_phi_report" type="select" label="Generate Philosopher Reports">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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377 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
378 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
379 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
380 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
381 <section name="phi_report_opts" expanded="false" title="FDR Filter and Report">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
382 <param name="dont_use_prot_prophet_file" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
383 <param name="print_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
384 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
385 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
386 <when value="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
387 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
388 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
389
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
390 <!-- Set Philosopher Report (phi-report) workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
391 <token name="@PHIREPORT@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
392 #set $prfx = $wf.validation.validation_tab.phi_report
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
393 #if $prfx.run_phi_report == 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
394 #set $wfdict['phi-report.run-report'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
395 #set $prfx = $wf.validation.validation_tab.phi_report.phi_report_opts
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
396 #set $wfdict['phi-report.print-decoys'] = $prfx.print_decoys
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
397 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
398 #set $wfdict['phi-report.run-report'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
399 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
400 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
401
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
402 <!-- PeptideProphet options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
403 <xml name="peptide_prophet" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
404 <section name="peptide_prophet" expanded="true" title="PeptideProphet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
405 <param name="combined_pepxml" type="boolean" truevalue="true" falsevalue="false" checked="@COMBINED_PEPXML@" label="Single combined pepxml per experiment or group"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
406 <param argument="--decoyprobs" type="boolean" truevalue="--decoyprobs" falsevalue="" checked="@DECOYPROBS@" label="compute possible non-zero probabilities for Decoy entries on the last iteration"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
407 <param argument="--ppm" type="boolean" truevalue="--ppm" falsevalue="" checked="@PPM@" label="use PPM mass error instead of Dalton for mass modeling"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
408 <param argument="--accmass" type="boolean" truevalue="--accmass" falsevalue="" checked="@ACCMASS@" label="use Accurate Mass model binning"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
409 <param argument="--nonparam" type="boolean" truevalue="--nonparam" falsevalue="" checked="@NONPARAM@" label="use semi-parametric modeling, must be used in conjunction with --decoy option"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
410 <param argument="--expectscore" type="boolean" truevalue="--expectscore" falsevalue="" checked="@EXPECTSCORE@" label="use expectation value as the only contributor to the f-value for modeling"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
411 <param argument="--masswidth" type="float" value="@MASSWIDTH@" label="model mass width (default 5)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
412 <param argument="--clevel" type="integer" value="@CLEVEL@" label="set Conservative Level in neg_stdev from the neg_mean, low numbers are less conservative, high numbers are more conservative"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
413 <param argument="--glyc" type="boolean" truevalue="--glyc" falsevalue="" checked="false" label="enable peptide Glyco motif model"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
414 <param argument="--combine" type="boolean" truevalue="--combine" falsevalue="" checked="false" label="combine the results from PeptideProphet into a single result file" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
415 <param argument="--minpeplen" type="integer" value="7" label="minimum peptide length not rejected (default 7)" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
416 <param argument="--minprob" type="float" value="0.05" label="report results with minimum probability" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
417 <param argument="--nomass" type="boolean" truevalue="--nomass" falsevalue="" checked="false" label="disable mass model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
418 <param argument="--nonmc" type="boolean" truevalue="--nonmc" falsevalue="" checked="false" label="disable NMC missed cleavage model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
419 <param argument="--nontt" type="boolean" truevalue="--nontt" falsevalue="" checked="false" label="disable NTT enzymatic termini model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
420 <param argument="--phospho" type="boolean" truevalue="--phospho" falsevalue="" checked="false" label="enable peptide phospho motif model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
421 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
422 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
423 <token name="@PEPTIDEPROPHET@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
424 #set $prfx = $wf.validation.validation_tab.psm_validation.peptide_prophet
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
425 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
426 #set $wfdict['peptide-prophet.combine-pepxml'] = str($prfx.combined_pepxml)
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
427 #set $cmd_opts = [str($prfx.accmass),str($prfx.combine),str($prfx.decoyprobs),str($prfx.expectscore),str($prfx.glyc),str($prfx.nomass),str($prfx.nonmc),str($prfx.nonparam),str($prfx.nontt),str($prfx.phospho),str($prfx.ppm)]
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
428 #silent $cmd_opts.append('--clevel ' + str($prfx.clevel))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
429 #silent $cmd_opts.append('--masswidth ' + str($prfx.masswidth))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
430 #silent $cmd_opts.append('--minpeplen ' + str($prfx.minpeplen))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
431 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
432 #set $wfdict['peptide-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
433 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
434
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
435 <!-- CrystalC options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
436 <xml name="crystalc">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
437 <param name="run_crystalc" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Run Crystal-C" help="Recommend for open searches for additional resuts cleanup"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
438 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
439
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
440 <!-- Protein Prophet options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
441 <xml name="protein_prophet" token_minprob="0.05">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
442 <conditional name="protein_prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
443 <param name="run_protein_prophet" type="select" label="Run Protein Prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
444 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
445 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
446 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
447 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
448 <section name="protein_prophet_opts" expanded="true" title="Protein Prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
449 <param argument="--iprophet" type="boolean" truevalue="--iprophet" falsevalue="" checked="false" label="input is from iProphet" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
450 <param argument="--maxppmdiff" type="integer" value="2000000" label="maximum peptide mass difference in ppm (default 2000000)" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
451 <param argument="--minprob" type="float" value="@MINPROB@" label="PeptideProphet probability threshold (default 0.05)" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
452 <param argument="--nonsp" type="boolean" truevalue="--nonsp" falsevalue="" checked="false" label="do not use NSP model" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
453 <param argument="--subgroups" type="boolean" truevalue="--subgroups" falsevalue="" checked="false" label="do not use NOGROUPS" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
454 <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="report results for UNMAPPED proteins" />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
455 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
456 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
457 <when value="false"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
458 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
459 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
460
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
461 <!-- Set ProteinProphet workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
462 <token name="@PROTEINPROPHET@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
463 #set $prfx = $wf.validation.validation_tab.protein_prophet
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
464 #if $prfx.run_protein_prophet == 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
465 #set $prfx = $wf.validation.validation_tab.protein_prophet.protein_prophet_opts
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
466 #set $wfdict['protein-prophet.run-protein-prophet'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
467 #set $cmd_opts = [str($prfx.iprophet),str($prfx.nonsp),str($prfx.subgroups),str($prfx.unmapped)]
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
468 #silent $cmd_opts.append('--maxppmdiff ' + str($prfx.maxppmdiff))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
469 #silent $cmd_opts.append('--minprob ' + str($prfx.minprob))
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
470 #set $wfdict['protein-prophet.cmd-opts'] = ' '.join($cmd_opts).strip()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
471 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
472 #set $wfdict[protein-prophet.run-protein-prophet] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
473 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
474 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
475
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
476 <!-- Validation options. Includes PeptideProphet, Percolator, MSBooster, ProteinProphet, and CrystalC -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
477 <xml name="validation" token_expand="false" token_pep="false" token_perc="false" token_boost="false" token_no="true" token_masswidth="5" token_clevel="0" token_accmass="true" token_decoyprobs="true" token_nonparam="true" token_expectscore="true" token_ppm="true" token_combined_pepxml="false" token_protp_minprob="0.05">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
478 <section name="validation" expanded="@EXPAND@" title="Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
479 <conditional name="validation_tab">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
480 <param name="run_validation" type="select" label="Run Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
481 <option value="true" selected="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
482 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
483 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
484 <when value="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
485 <yield/> <!-- crystalc -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
486 <conditional name="psm_validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
487 <param name="run_psm_validation" type="select" label="PSM Validation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
488 <option value="peptide_prophet" selected="@PEP@">Run PeptideProphet</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
489 <option value="percolator" selected="@PERC@">Run Percolator</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
490 <option value="msbooster_percolator" selected="@BOOST@">Run MSBooster and Percolator</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
491 <option value="no" selected="@NO@">Use workflow values</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
492 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
493 <when value="peptide_prophet">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
494 <expand macro="peptide_prophet" masswidth="@MASSWIDTH@" clevel="@CLEVEL@" accmass="@ACCMASS@" decoyprobs="@DECOYPROBS@" nonparam="@NONPARAM@" expectscore="@EXPECTSCORE@" ppm="@PPM@" combined_pepxml="@COMBINED_PEPXML@"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
495 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
496 <when value="percolator">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
497 <expand macro="percolator"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
498 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
499 <when value="msbooster_percolator">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
500 <expand macro="msbooster"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
501 <expand macro="percolator"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
502 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
503 <when value="no">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
504 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
505 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
506 <expand macro="protein_prophet" minprob="@PROTP_MINPROB@"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
507 <expand macro="phi_report"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
508 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
509 <when value="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
510 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
511 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
512 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
513 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
514
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
515 <!-- Set validation workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
516 <token name="@VALIDATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
517 #set $prfx = $wf.validation.validation_tab.psm_validation
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
518 #if $prfx.run_psm_validation == 'peptide_prophet'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
519 #set $wfdict['run-psm-validation'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
520 #set $wfdict['msbooster.run-msbooster'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
521 #set $wfdict['percolator.run-percolator'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
522 @PEPTIDEPROPHET@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
523 #elif $prfx.run_psm_validation == 'percolator'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
524 #set $wfdict['run-psm-validation'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
525 #set $wfdict['msbooster.run-msbooster'] = 'false'
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
526 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
527 @PERCOLATOR@
4
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
528 #elif $prfx.run_psm_validation == 'msbooster_percolator'
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
529 #set $wfdict['run-psm-validation'] = 'true'
6
59fec1e2a6c3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 3fe4cafecf2b25f602915c638b0d6993d957e1e6
galaxyp
parents: 5
diff changeset
530 #set $wfdict['peptide-prophet.run-peptide-prophet'] = 'false'
4
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
531 @MSBOOSTER@
e58fb5e6790a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit f98d62a3e8aef1dd26fa64eff5c19f5773652d43
galaxyp
parents: 3
diff changeset
532 @PERCOLATOR@
0
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
533 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
534 @PROTEINPROPHET@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
535 @PHIREPORT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
536 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
537
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
538 <!-- PTM-Sheperd options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
539 <xml name="ptm_shepherd" token_expand="false" token_yes="true" token_no="false" token_a="false" token_b="true" token_c="false" token_x="false" token_y="true" token_z="false" token_unimod="true" token_common="false" token_glyco="false" token_custom="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
540 <section name="ptms" expanded="false" title="PTMs">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
541 <conditional name="ptm_shepherd">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
542 <param name="run_ptm_shepherd" type="select" label="Run PTM Shepherd">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
543 <option value="yes" selected="@YES@">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
544 <option value="no" selected="@NO@">no</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
545 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
546 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
547 <param name="output_extended" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extended output"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
548 <section name="ptm_profiling" expanded="false" title="PTM Profiling">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
549 <param name="histo_smoothbins" type="integer" value="" min="0" optional="true" label="Smoothing factor" help="ptmshepherd.histo_smoothbins"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
550 <param name="precursor_mass_units" type="select" label="Precursor Mass tolerance units" help="ptmshepherd.precursor_mass_units">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
551 <option value="1" selected="true">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
552 <option value="0" selected="false">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
553 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
554 <param name="precursor_tol" type="float" value="" min="0" optional="true" label="Precursor tolerance" help="ptmshepherd.precursor_tol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
555 <param name="peakpicking_promRatio" type="float" value="" min="0" optional="true" label="Prominece ratio" help="ptmshepherd.peakpicking_promRatio"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
556 <param name="peakpicking_mass_units" type="select" label="Peakpicking Mass tolerance units" help="ptmshepherd.peakpicking_mass_units">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
557 <option value="1" selected="true">ppm</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
558 <option value="0" selected="false">Daltons</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
559 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
560 <param name="peakpicking_width" type="float" value="" min="0" optional="true" label="Peak picking width" help="ptmshepherd.peakpicking_width"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
561 <param name="peakpicking_minPsm" type="integer" value="" min="0" optional="true" label="Peak minimum PSMs" help="ptmshepherd.peakpicking_minPsm"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
562 <param name="spectra_ppmtol" type="float" value="" min="0" optional="true" label="Fragment Mass tolerance (PPM)" help="ptmshepherd.spectra_ppmtol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
563 <param name="normalization" type="select" optional="true" label="Normalize data to" help="ptmshepherd.normalization-psms ptmshepherd.normalization-scans">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
564 <option value="psms" selected="true">PSMs</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
565 <option value="scans" selected="false">MS2 scans</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
566 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
567 <param name="varmod_masses" type="select" optional="true" label="Custom mass shifts" help="ptmshepherd.varmod_masses">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
568 <option value="Failed_Carbamidomethylation\:-57.021464">Failed_Carbamidomethylation:-57.021464</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
569 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
570 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
571 <section name="ptm_annotation" expanded="true" title="PTM Annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
572 <param name="annotation_tol" type="float" value="" min="0" optional="true" label="Annotation tolerance (Da)" help="ptmshepherd.annotation_tol"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
573 <conditional name="annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
574 <param name="annotation_source" type="select" label="Annotation source" help="ptmshepherd.annotation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
575 <option value="unimod" selected="@UNIMOD@">Unimod</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
576 <option value="common" selected="@COMMON@">Common mass shifts</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
577 <option value="glyco" selected="@GLYCO@">Glyco mass shifts</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
578 <option value="custom" selected="@CUSTOM@">Custom annotation file</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
579 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
580 <when value="unimod"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
581 <when value="common"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
582 <when value="glyco"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
583 <when value="custom">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
584 <param name="annotation_file" type="data" format="txt" label="Custom annotation file"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
585 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
586 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
587 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
588 <section name="ptm_localization" expanded="false" title="PTM Localization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
589 <param name="nions" type="select" multiple="true" optional="true" label="Use specified N-term ions" help="(default: a,b for CID, c for ETD)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
590 <option value="a" selected="@A@">a</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
591 <option value="b" selected="@B@">b</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
592 <option value="c" selected="@C@">c</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
593 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
594 <param name="cions" type="select" multiple="true" optional="true" label="use specified C-term ions" help="(default: y for CID, z for ETD)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
595 <option value="x" selected="@X@">x</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
596 <option value="y" selected="@Y@">y</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
597 <option value="z" selected="@Z@">z</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
598 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
599 <param name="spectra_maxfragcharge" type="integer" value="" min="0" optional="true" label="Max fragment charge" help="ptmshepherd.spectra_maxfragcharge"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
600 <param name="localization_background" type="integer" value="" min="0" optional="true" label="Localization background" help="ptmshepherd.localization_background"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
601 <param name="localization_allowed_res" type="select" label="Restrict localization to" help="ptmshepherd.localization_allowed_res">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
602 <option value="" selected="true">none</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
603 <option value="all">all</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
604 <option value="N">N</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
605 <option value="ST">ST</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
606 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
607 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
608 <!-- Not yet implemented
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
609 <section name="ion_discovery" expanded="false" title="Diagnostic Ion Discovery">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
610 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
611 <section name="glycan" expanded="false" title="Gyclan Assignment and FDR">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
612 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
613 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
614 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
615 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
616 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
617 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
618 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
619
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
620 <!-- Set PTM-Sheperd workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
621 <token name="@PTM_SHEPHERD@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
622 #set $prfx = $wf.ptms.ptm_shepherd
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
623 #if $prfx.run_ptm_shepherd == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
624 #set $wfdict['ptmshepherd.run-shepherd'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
625 #set $cxt = $prfx.ptm_profiling
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
626 #set $wfdict['ptmshepherd.output_extended'] = $prfx.output_extended
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
627 #if $cxt.histo_smoothbins != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
628 #set $wfdict['ptmshepherd.histo_smoothbins'] = $cxt.histo_smoothbins
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
629 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
630 #if $cxt.precursor_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
631 #set $wfdict['ptmshepherd.precursor_mass_units'] = $ctx.precursor_mass_units
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
632 #set $wfdict['ptmshepherd.precursor_tol'] = $cxt.precursor_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
633 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
634 #if $cxt.peakpicking_promRatio != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
635 #set $wfdict['ptmshepherd.peakpicking_promRatio'] = $cxt.peakpicking_promRatio
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
636 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
637 #if $cxt.peakpicking_width != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
638 #set $wfdict['ptmshepherd.peakpicking_mass_units'] = $ctx.peakpicking_mass_units
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
639 #set $wfdict['ptmshepherd.peakpicking_width'] = $cxt.peakpicking_width
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
640 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
641 #if $cxt.peakpicking_minPsm != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
642 #set $wfdict['ptmshepherd.peakpicking_minPsm'] = $cxt.peakpicking_minPsm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
643 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
644 #if $cxt.spectra_ppmtol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
645 #set $wfdict['ptmshepherd.spectra_ppmtol'] = $cxt.spectra_ppmtol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
646 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
647 #if $cxt.normalization != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
648 #if $cxt.normalization == "psms"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
649 #set $wfdict['ptmshepherd.normalization-psms'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
650 #set $wfdict['ptmshepherd.normalization-scans'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
651 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
652 #set $wfdict['ptmshepherd.normalization-psms'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
653 #set $wfdict['ptmshepherd.normalization-scans'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
654 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
655 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
656 #if $cxt.varmod_masses != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
657 #set $wfdict['ptmshepherd.varmod_masses'] = $cxt.varmod_masses
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
658 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
659 #set $cxt = $prfx.ptm_annotation
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
660 #if $cxt.annotation_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
661 #set $wfdict['ptmshepherd.annotation_tol'] = $cxt.annotation_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
662 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
663 #if $cxt.annotation.annotation_source == 'unimod'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
664 #set $wfdict['ptmshepherd.annotation-unimod'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
665 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
666 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
667 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
668 #elif $cxt.annotation.annotation_source == 'common'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
669 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
670 #set $wfdict['ptmshepherd.annotation-common'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
671 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
672 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
673 #elif $cxt.annotation.annotation_source == 'glyco'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
674 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
675 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
676 #set $wfdict['ptmshepherd.annotation-glyco'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
677 #set $wfdict['ptmshepherd.annotation-custom'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
678 #elif $cxt.annotation.annotation_source == 'custom'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
679 #set $wfdict['ptmshepherd.annotation-unimod'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
680 #set $wfdict['ptmshepherd.annotation-common'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
681 #set $wfdict['ptmshepherd.annotation-glyco'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
682 #set $wfdict['ptmshepherd.annotation-custom'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
683 #set $wfdict['ptmshepherd.annotation_file'] = $cxt.annotation.annotation_file
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
684 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
685 #set $cxt = $prfx.ptm_localization
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
686 #if $cxt.nions is not None
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
687 #set $wfdict['ptmshepherd.iontype_a'] = str('a' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
688 #set $wfdict['ptmshepherd.iontype_b'] = str('b' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
689 #set $wfdict['ptmshepherd.iontype_c'] = str('c' in $cxt.nions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
690 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
691 #if $cxt.cions is not None
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
692 #set $wfdict['ptmshepherd.iontype_x'] = str('x' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
693 #set $wfdict['ptmshepherd.iontype_y'] = str('y' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
694 #set $wfdict['ptmshepherd.iontype_z'] = str('z' in $cxt.cions).lower()
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
695 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
696 #if $cxt.spectra_maxfragcharge != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
697 #set $wfdict['ptmshepherd.spectra_maxfragcharge'] = $cxt.spectra_maxfragcharge
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
698 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
699 #if $cxt.localization_background != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
700 #set $wfdict['ptmshepherd.localization_background'] = $cxt.localization_background
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
701 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
702 #set $wfdict['ptmshepherd.localization_allowed_res'] = $cxt.localization_allowed_res
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
703 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
704 #set $wfdict['ptmshepherd.run-shepherd'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
705 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
706 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
707
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
708 <token name="@RE_EXCLUDEMOD@">@RE_AA@,@RE_FLOAT@</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
709 <token name="@RE_EXCLUDEMODS@">@RE_EXCLUDEMOD@(;\s*@RE_EXCLUDEMOD@)*</token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
710
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
711 <!-- Label-free quantification options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
712 <xml name="label_free_quantification" token_expand="false">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
713 <section name="quant_ms1" expanded="@EXPAND@" title="Quant (MS1)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
714 <conditional name="label_free_quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
715 <param name="label_free_quantification_run" type="select" label="Perform Label-Free Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
716 <option value="default" selected="true">Use workflow default</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
717 <option value="no">No Label-Free Quantification</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
718 <option value="freequant">Run FreeQuant</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
719 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
720 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
721 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
722 <when value="freequant">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
723 <section name="freequant" expanded="false" title="IonQuant Label-Free Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
724 <param name="rt_tol" type="float" value="" min="0" optional="true" label="RT Window (minutes)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
725 <param name="mz_tol" type="integer" value="" min="1" optional="true" label="m/z Window (ppm)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
726 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
727 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
728 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
729 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
730 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
731
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
732 <!-- Set label-free quantification workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
733 <token name="@LABEL_FREE_QUANTIFICATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
734 #set $prfx = $wf.quant_ms1.label_free_quantification
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
735 #if $prfx.label_free_quantification_run == 'no'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
736 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
737 #elif $prfx.label_free_quantification_run == 'freequant'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
738 #set $wfdict['quantitation.run-label-free-quant'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
739 #set $wfdict['ionquant.run-ionquant'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
740 #set $wfdict['freequant.run-freequant'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
741 #set $cxt = $prfx.freequant
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
742 #if $cxt.rt_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
743 #set $wfdict['freequant.rt-tol'] = $cxt.rt_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
744 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
745 #if $cxt.mz_tol != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
746 #set $wfdict['freequant.mz-tol'] = $cxt.mz_tol
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
747 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
748 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
749 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
750
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
751 <!--
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
752 Isobaric quantification options
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
753
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
754 TMT-n uses the following n first labels from TMT-18
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
755 TMT-18 "126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
756 iTRAQ-4 "114, 115, 116, 117"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
757 iTRAQ-8 "113, 114, 115, 116, 117, 118, 119, 121"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
758 -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
759 <xml name="isobaric_quantification" token_expand="false" token_yes="true" token_no="false" token_plex="" token_level="2" token_virtual="false" token_pool="false" token_bridge="true">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
760 <section name="quant_iso" expanded="@EXPAND@" title="Quant (Isobaric)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
761 <conditional name="isobaric_quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
762 <param name="isobaric_quantification_step" type="select" label="Perform Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
763 <option value="default">Use workflow defaults</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
764 <option value="yes" selected="@YES@">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
765 <option value="no" selected="@NO@">no</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
766 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
767 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
768 <when value="no"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
769 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
770 <section name="options" expanded="true" title="Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
771 <param name="quant_level" type="integer" value="@LEVEL@" min="1" max="3" label="MS level for the quantification"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
772 <param name="channel_num" type="text" value="@PLEX@" optional="true" label="Number of channels">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
773 <validator type="regex" message="">^TMT-\d?</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
774 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
775 <param name="ref_tag" type="select" label="Set Unique tag to identify reference channels">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
776 <help>Virtual or specify a Reference sample tag: pool or Bridge</help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
777 <option value="Virtual" selected="@VIRTUAL@">Virtual - Add an artificial reference channel</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
778 <option value="pool" selected="@POOL@">pool</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
779 <option value="Bridge" selected="@BRIDGE@">Bridge</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
780 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
781 <param name="groupby" type="select" optional="true" label="Group by level of summarization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
782 <option value="0">Gene level</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
783 <option value="1">Protein</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
784 <option value="2">Peptide sequence</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
785 <option value="3">Multiple PTM sites</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
786 <option value="4">Single PTM site</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
787 <option value="-1">All</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
788 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
789 <param name="log2transformed" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Log2 transform the intensity"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
790 <param name="prot_norm" type="select" optional="true" label="normalization">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
791 <option value="0">None</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
792 <option value="1">MC (median centering)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
793 <option value="2">GN (median centering + variance scaling)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
794 <option value="-1">generate reports with all normalization options</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
795 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
796 <conditional name="glycan_conditional">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
797 <param name="use_glycan_composition" type="select" label="Perform Isobaric Quantification">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
798 <option value="default">Use workflow defaults</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
799 <option value="yes">yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
800 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
801 <when value="default"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
802 <when value="yes">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
803 <param name="mod_tag" type="select" optional="true" label="PTM Mod tag">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
804 <option value="none">none</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
805 <option value="N-glyco">N-glyco</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
806 <option value="C(239.1629)">C(239.1629)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
807 <option value="K(-187.1524)">K(-187.1524)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
808 <option value="K(-262.1966)">K(-262.1966)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
809 <option value="K(114.0429),K(-115.12)">K(114.0429),K(-115.12)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
810 <option value="S(79.9663),T(79.9663),Y(79.9663)">S(79.9663),T(79.9663),Y(79.9663)</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
811 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
812 <param name="min_site_prob" type="float" min="-1.0" max="1.0" optional="true" label="Minimum site probability">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
813 <help>site localization confidence thresholdr: -1 for global, 0 for search engine determined, above 0 for probability</help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
814 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
815 <param name="glyco_qval" type="integer" value="-1" optional="true" label="Glycan FDR filter"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
816 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
817 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
818 <param name="unique_gene" type="select" optional="true" label="Peptide-Gene uniqueness">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
819 <option value="0">0: allow all PSMs</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
820 <option value="1">1: remove PSMs mapping to more than one GENE with evidence of expression in the dataset</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
821 <option value="2">2: remove all PSMs mapping to more than one GENE in the fasta file</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
822 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
823 <param name="unique_pep" type="select" optional="true" label="Peptide-Protein uniqueness">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
824 <option value="false">unique plus razor peptides</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
825 <option value="true">allow PSMs with unique peptides only</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
826 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
827 <param name="min_pep_prob" type="float" min="0" max="1.0" optional="true" label="only use PSMs with a minimum probability score"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
828 help="minimum PSM probability threshold (in addition to FDR-based filtering by Philosopher)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
829 <param name="min_purity" type="float" min="0" max="1.0" optional="true" label="ion purity threshold (default 0.5)"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
830 <param name="min_percent" type="float" min="0" max="1.0" optional="true" label="ignore the lower % PSMs based on their summed abundances"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
831 help="e.g. value of 0.05 indicates removal of PSMs with the summed TMT reporter ions intensity in the lowest 5% of all PSMs"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
832 <param name="max_pep_prob_thres" type="float" min="0" max="1.0" optional="true" label="threshold for maximum peptide probability"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
833 <param name="min_ntt" type="integer" min="0" max="2" optional="true" label="minimum allowed number of enzymatic termini"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
834 <param name="aggregation_method" type="select" optional="true" label="the aggregation method from the PSM level to the specified level">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
835 <option value="0">0: median</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
836 <option value="1">1: weighted-ratio</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
837 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
838 <param name="prot_exclude" type="text" optional="true" label="Exclude proteins with specified tags at the beginning of the accession number"
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
839 help="e.g. none: no exclusion; sp|,tr| : exclude protein with sp| or tr|">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
840 <validator type="regex">^(none|[a-zA-Z]+\|)$</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
841 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
842 <param name="best_psm" type="select" optional="true" label="keep the best PSM only (highest summed TMT intensity) among all redundant PSMs within the same LC-MS run">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
843 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
844 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
845 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
846 <param name="psm_norm" type="select" optional="true" label="perform additional retention time-based normalization at the PSM level">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
847 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
848 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
849 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
850 <param name="allow_overlabel" type="select" optional="true" label="allow PSMs with TMT on S (when overlabeling on S was allowed in the database search)">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
851 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
852 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
853 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
854 <param name="allow_unlabeled" type="select" optional="true" label="allow PSMs without TMT tag or acetylation on the peptide n-terminus">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
855 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
856 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
857 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
858 <param name="outlier_removal" type="select" optional="true" label="perform outlier removal">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
859 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
860 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
861 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
862 <param name="ms1_int" type="select" optional="true" label="MS1 precursor ion intensity for reference sample abundance estimation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
863 <option value="true">Yes - use MS1 precursor ion intensity</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
864 <option value="false">No - use MS2 reference intensity</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
865 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
866 <param name="tolerance" type="integer" optional="true" label="Tolerance"/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
867 <param name="top3_pep" type="select" optional="true" label="use top 3 most intense peptide ions as part of the reference sample abundance estimation">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
868 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
869 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
870 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
871 <param name="print_RefInt" type="select" optional="true" label="print individual reference sample abundance estimates for each multiplex in the final reports">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
872 <option value="false">No</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
873 <option value="true">Yes</option>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
874 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
875 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
876 </when>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
877 </conditional>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
878 </section>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
879 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
880
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
881 <!-- Set isobaric quantification workflow options -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
882 <token name="@ISOBARIC_QUANTIFICATION@"><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
883 #set $prfx = $wf.quant_iso.isobaric_quantification
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
884 #if $prfx.isobaric_quantification_step == 'no'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
885 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
886 #elif $prfx.isobaric_quantification_step == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
887 #set $wfdict['tmtintegrator.run-tmtintegrator'] = 'true'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
888 #set $wfdict['tmtintegrator.dont-run-fq-lq'] = 'false'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
889 #set $cxt = $prfx.options
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
890 #set $wfdict['tmtintegrator.quant_level'] = $cxt.quant_level
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
891 #set $wfdict['tmtintegrator.channel_num'] = $cxt.channel_num
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
892 #if $cxt.ref_tag == 'Virtual'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
893 #set $wfdict['tmtintegrator.add_Ref'] = -1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
894 #else
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
895 #set $wfdict['tmtintegrator.add_Ref'] = 1
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
896 #set $wfdict['tmtintegrator.ref_tag'] = $cxt.ref_tag
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
897 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
898 #if $cxt.groupby != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
899 #set $wfdict['tmtintegrator.groupby'] = $cxt.groupby
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
900 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
901 #set $wfdict['tmtintegrator.log2transformed'] = $cxt.log2transformed
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
902 #if $cxt.prot_norm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
903 #set $wfdict['tmtintegrator.prot_norm'] = $cxt.prot_norm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
904 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
905 #if $cxt.glycan_conditional.use_glycan_composition == 'yes'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
906 #if $cxt.glycan_conditional.mod_tag != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
907 #set $wfdict['tmtintegrator.mod_tag'] = $cxt.glycan_conditional.mod_tag
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
908 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
909 #if $cxt.glycan_conditional.min_site_prob != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
910 #set $wfdict['tmtintegrator.min_site_prob'] = $cxt.glycan_conditional.min_site_prob
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
911 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
912 #if $cxt.glycan_conditional.glyco_qval != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
913 #set $wfdict['tmtintegrator.glyco_qval'] = $cxt.glycan_conditional.glyco_qval
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
914 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
915 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
916 #if $cxt.unique_gene != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
917 #set $wfdict['tmtintegrator.unique_gene'] = $cxt.unique_gene
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
918 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
919 #if $cxt.unique_pep != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
920 #set $wfdict['tmtintegrator.unique_pep'] = $cxt.unique_pep
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
921 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
922 #if $cxt.min_pep_prob != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
923 #set $wfdict['tmtintegrator.min_pep_prob'] = $cxt.min_pep_prob
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
924 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
925 #if $cxt.min_purity != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
926 #set $wfdict['tmtintegrator.min_purity'] = $cxt.min_purity
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
927 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
928 #if $cxt.min_percent != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
929 #set $wfdict['tmtintegrator.min_percent'] = $cxt.min_percent
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
930 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
931 #if $cxt.max_pep_prob_thres != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
932 #set $wfdict['tmtintegrator.max_pep_prob_thres'] = $cxt.max_pep_prob_thres
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
933 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
934 #if $cxt.min_ntt != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
935 #set $wfdict['tmtintegrator.min_ntt'] = $cxt.min_ntt
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
936 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
937 #if $cxt.aggregation_method != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
938 #set $wfdict['tmtintegrator.aggregation_method'] = $cxt.aggregation_method
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
939 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
940 #if $cxt.prot_exclude != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
941 #set $wfdict['tmtintegrator.prot_exclude'] = $cxt.prot_exclude
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
942 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
943 #if $cxt.best_psm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
944 #set $wfdict['tmtintegrator.best_psm'] = $cxt.best_psm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
945 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
946 #if $cxt.psm_norm != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
947 #set $wfdict['tmtintegrator.psm_norm'] = $cxt.psm_norm
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
948 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
949 #if $cxt.allow_overlabel != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
950 #set $wfdict['tmtintegrator.allow_overlabel'] = $cxt.allow_overlabel
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
951 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
952 #if $cxt.allow_unlabeled != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
953 #set $wfdict['tmtintegrator.allow_unlabeled'] = $cxt.allow_unlabeled
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
954 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
955 #if $cxt.outlier_removal != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
956 #set $wfdict['tmtintegrator.outlier_removal'] = $cxt.outlier_removal
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
957 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
958 #if $cxt.ms1_int != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
959 #set $wfdict['tmtintegrator.ms1_int'] = $cxt.ms1_int
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
960 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
961 #if $cxt.tolerance != ''
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
962 #set $wfdict['tmtintegrator.tolerance'] = $cxt.tolerance
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
963 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
964 #if $cxt.top3_pep != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
965 #set $wfdict['tmtintegrator.top3_pep'] = $cxt.top3_pep
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
966 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
967 #if $cxt.print_RefInt != 'None'
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
968 #set $wfdict['tmtintegrator.print_RefInt'] = $cxt.print_RefInt
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
969 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
970 #end if
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
971 ]]></token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
972
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
973 <!-- License agreement texts. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
974 <token name="@MSFRAGGER_LICENSE_AGREEMENT@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
975 MSFragger is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: http://msfragger-upgrader.nesvilab.org/upgrader/MSFragger-LICENSE.pdf. This license provides with non-exclusive, non-transferable right to use MSFragger solely for academic research, non-commercial or educational purposes. I agree to be subject to the terms and conditions of this license. I understand that to use MSFragger for other purposes requires a commercial license from the University of Michigan Office of Tech Transfer.
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
976 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
977 <token name="@IONQUANT_LICENSE_AGREEMENT@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
978 IonQuant is available freely for academic research and educational purposes only. I have read the ACADEMIC license for MSFragger software: https://msfragger.arsci.com/ionquant/IonQuant%20Academic%20Use%20License%2005162022.pdf
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
979 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
980 <token name="@THERMO_RAW_READER_LICENSE_AGREEMENT@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
981 I agree to the terms of Thermo (c) Raw File Reader License Agreement: http://msfragger-upgrader.nesvilab.org/upgrader/RawFileRdr_License_Agreement_RevA.pdf
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
982 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
983 <token name="@BRUKER_LICENSE_AGREEMENT@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
984 I agree to the terms of Bruker SDK library distribution conditions: http://msfragger-upgrader.nesvilab.org/upgrader/redist.txt
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
985 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
986 <token name="@LICENSE_AGREEMENTS@">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
987 @MSFRAGGER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
988 @IONQUANT_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
989 @THERMO_RAW_READER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
990 @BRUKER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
991 </token>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
992
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
993 <!-- User must check box agreeing to MSFragger license agreement. -->
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
994 <xml name="license_agreements">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
995 <param name="license_agreements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="I understand that these tools, including MSFragger, IonQuant, Bruker, and Thermo Raw File Reader, are available freely for academic research and educational purposes only, and agree to the following terms.">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
996 <validator type="expression" message="You must agree to the MSFragger license!">value == True</validator>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
997 <help><![CDATA[
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
998 @MSFRAGGER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
999 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1000 @IONQUANT_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1001 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1002 @THERMO_RAW_READER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1003 <br/><br/>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1004 @BRUKER_LICENSE_AGREEMENT@
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1005 ]]></help>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1006 </param>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1007 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1008
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1009 <xml name="citations">
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1010 <citations>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1011 <citation type="doi">10.1038/s41592-020-0912-y</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1012 <citation type="doi">10.1038/nmeth.4256</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1013 <citation type="doi">10.1038/s41467-020-17921-y</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1014 <citation type="doi">10.1038/s41592-020-0967-9</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1015 <citation type="doi">10.1021/acs.jproteome.0c00119</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1016 <citation type="doi">10.1074/mcp.TIR120.002216</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1017 <citation type="doi">10.1074/mcp.TIR120.002048</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1018 <citation type="doi">10.1016/j.mcpro.2021.100077</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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parents:
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1019 <citation type="doi">10.1021/acs.jproteome.0c00544</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1020 <citation type="doi">10.1038/nmeth.3255</citation>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1021 <yield />
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1022 </citations>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
parents:
diff changeset
1023 </xml>
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
galaxyp
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diff changeset
1024 </macros>