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1 <tool id="maxquant" version="0.1.0" name="MaxQuant">
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2 <description>
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3 </description>
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4 <requirements>
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5 <requirement>maxquant</requirement>
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6 <requirement type="platform">windows</requirement>
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7 </requirements>
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8 <configfiles>
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9 <configfile name="inputs_config">##Describe inputs
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10 #set $type = str($analysis_type.type)
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11 #if $type == "single"
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12 #set $groups = [$analysis_type]
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13 #elif $type == "multi_same"
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14 #set $groups = $analysis_type.groups
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15 #end if
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16 #for $i, $group in enumerate($groups)
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17 num:${str(i + 1)}
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18 #for $input in $group.inputs
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19 name:${input.display_name}
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20 path:${input}
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21 #end for
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22 #end for
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23 </configfile>
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24 </configfiles>
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25 <command interpreter="python">maxquant_wrapper.py
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26 --input_groups=$inputs_config
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27 --database="${database}"
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28 --database_name="${database.name}"
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29 --protease=$analysis_type.protease
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30 --first_search_tol=$analysis_type.first_search_tol
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31 --main_search_tol=$analysis_type.main_search_tol
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32 --max_missed_cleavages=$analysis_type.max_missed_cleavages
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33 --max_n_mods=$analysis_type.max_n_mods
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34 --variable_mods="${analysis_type.variable_modifications or ''}"
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35 #if $analysis_type.advanced_group_parameters.specify
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36 --do_mass_filtering=$analysis_type.advanced_group_parameters.do_mass_filtering
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37 --max_charge=$analysis_type.advanced_group_parameters.max_charge
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38 #end if
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39 #set $run = $analysis_type.run
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40 #set $lcms_run_type = $run.lcms_run_type
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41 --lcms_run_type=$lcms_run_type
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42 #if str($lcms_run_type) != "3"
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43 ## i.e. is not reporter ion type
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44 #if $run.labels_conditional.labeled
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45 #for $label_group in $run.labels_conditional.label_groups
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46 --labels="${label_group.labels or ''}"
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47 #end for
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48 --max_labeled_aa=$run.labels_conditional.max_labeled_aa
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49 #end if
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50 #else
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51 --reporter_type=$run.reporter_type
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52 #end if
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53 #set $sp = $advanced_sequence_parameters
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54 #if $sp.specify
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55 --include_contamiants=${str(sp['include_contamiants']).lower()}
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56 --equal_il=${str(sp['equal_il']).lower()}
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57 --randomize=${str(sp['randomize'])}
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58 #end if
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59 #if $quantification.specify
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60 #set $restrict = $quantification.restrict.restrict_protein_quantification
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61 --restrict_protein_quantification=${str(restrict).lower()}
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62 #if $quantification.restrict.restrict_protein_quantification
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63 --restrict_mods="${quantification.restrict.restrict_modifications or ''}"
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64 #end if
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65 --quant_mode=$quantification.quant_mode
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66 --use_counterparts=$quantification.use_counterparts
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67 --min_ratio_count=$quantification.min_ratio_count
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68 #end if
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69 #if $site_quantification.specify
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70 --site_quant_mode=$site_quantification.site_quant_mode
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71 --use_norm_ratios_for_occupancy=$site_quantification.use_norm_ratios_for_occupancy
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72 #end if
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73 #set $identification_type = str($identification.options_type)
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74 #if $identification_type != "none"
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75 --protein_fdr=$identification.protein_fdr
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76 --peptide_fdr=$identification.peptide_fdr
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77 --site_fdr=$identification.site_fdr
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78 #if $identification_type != "simple"
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79 --peptide_pep=$identification.peptide_pep
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80 #end if
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81 #end if
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82 #if $misc.specify
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83 --re_quantify="$misc.re_quantify"
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84 #end if
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85 --fixed_mods="${fixed_modifications or ''}"
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86 --output_protein_groups=$output_protein_groups
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87 --output_peptides=$output_peptides
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88 --output_evidence=$output_evidence
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89 --output_parameters=$output_parameters
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90 --output_msms=$output_msms
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91 --output_mqpar=$output_mqpar
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92 </command>
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93 <macros>
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94 <macro name="input_param">
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95 <param format="raw" multiple="true" name="inputs" type="data" label="RAW Inputs" help="" />
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96 </macro>
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97 <macro name="mod_opts">
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98 <options from_file="maxquant_mods.loc">
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99 <column name="name" index="0"/>
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100 <column name="value" index="0" />
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101 </options>
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102 <sanitizer>
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103 <valid>
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104 <add value="<"/>
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105 <add value=">"/>
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106 <add value="["/>
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107 <add value="]"/>
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108 </valid>
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109 </sanitizer>
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110 </macro>
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111 <macro name="protease_opts">
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112 <options from_file="maxquant_proteases.loc">
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113 <column name="name" index="0"/>
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114 <column name="value" index="0" />
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115 </options>
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116 </macro>
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117 <macro name="group_params">
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118 <param name="protease" label="Enzyme" type="select">
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119 <expand macro="protease_opts" />
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120 </param>
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121 <param name="first_search_tol" label="First Search Tolerance (ppm)" type="float" value="20" />
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122 <param name="main_search_tol" label="Main Search Tolerance (ppm)" type="float" value="6" />
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123 <param name="max_n_mods" type="integer" label="Maximum Number of Modifications per Peptide" value="5" />
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124 <param name="max_missed_cleavages" type="integer" label="Maximum Number of Missed Cleavages" value="2" />
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125 <param name="variable_modifications" label="Variable Modifications" type="select" multiple="true">
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126 <expand macro="mod_opts" />
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127 </param>
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128 <conditional name="run">
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129 <param name="lcms_run_type" type="select" label="Run Type">
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130 <option value="0">Standard</option>
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131 <option value="2">All ion fragmentation</option>
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132 <option value="3">Reporter ion</option>
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133 </param>
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134 <when value="0">
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135 <expand macro="labels" />
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136 </when>
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137 <when value="2">
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138 <expand macro="labels" />
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139 </when>
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140 <when value="3">
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141 <expand macro="reporter" />
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142 </when>
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143 </conditional>
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144 <conditional name="advanced_group_parameters">
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145 <param name="specify" type="boolean" label="Specify Advanced Group Parameters" checked="false" />
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146 <when value="false">
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147 </when>
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148 <when value="true">
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149 <param name="do_mass_filtering" type="boolean" label="Individual Peptide Mass Tolerances" checked="true" truevalue="true" falsevalue="false" />
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150 <param name="max_charge" type="integer" label="Maximum Charge" value="7" />
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151 <!--
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152 TODO: First charge protease, first charge mods.
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153 -->
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154 </when>
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155 </conditional>
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156 </macro>
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157 <macro name="labels">
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158 <conditional name="labels_conditional">
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159 <param name="labeled" type="boolean" label="Specify Labels" checked="false" />
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160 <when value="false">
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161 </when>
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162 <when value="true">
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163 <repeat name="label_groups" title="Label Groups">
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164 <param name="labels" type="select" title="Labels" multiple="true" help="Select none to describe unlabelled 'light labels'.">
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165 <option value="Arg6">Arg6</option>
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166 <option value="Arg10">Arg10</option>
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167 <option value="Lys4">Lys4</option>
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168 <option value="Lys6">Lys6</option>
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169 <option value="Lys8">Lys8</option>
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170 </param>
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171 </repeat>
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172 <param name="max_labeled_aa" type="integer" title="Max Labeled Amino Acids" value="3" />
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173 </when>
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174 </conditional>
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175 </macro>
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176 <macro name="reporter">
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177 <param name="reporter_type" type="select" label="Reporter Ions Type">
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178 <option value="itraq_4plex">4-plex iTRAQ</option>
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179 <option value="itraq_8plex">8-plex iTRAQ</option>
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180 <option value="tmt_2plex">2-plex TMT</option>
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181 <option value="tmt_6plex">6-plex TMT</option>
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182 </param>
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183 </macro>
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184 <macro name="advanced_group_conditional">
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185
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186 </macro>
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187 <macro name="advanced_sequences_conditional">
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188 <conditional name="advanced_sequence_parameters">
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189 <param name="specify" type="boolean" label="Specify Advanced Sequence Parameters" checked="false" />
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190 <when value="false">
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191 </when>
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192 <when value="true">
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193 <param name="include_contamiants" type="boolean" label="Include Contamiant Sequences" checked="true" />
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194 <param name="equal_il" type="boolean" label="I = L" checked="false" />
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195 <param name="randomize" type="select" label="Decoy Type">
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196 <option value="false" selected="true">Reverse</option>
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197 <option value="true">Randomize</option>
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198 </param>
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199 <!-- TODO: special_aas, KR -->
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200 </when>
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201 </conditional>
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202 </macro>
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203 <macro name="identification_conditional">
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204 <conditional name="identification">
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205 <param name="options_type" type="select" label="Specify Identification Parameters">
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206 <option value="none">None, use all defaults.</option>
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207 <option value="simple">Simple, specify a few high level parameters.</option>
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208 <option value="advanced">Advanced, specify many identification parameters.</option>
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209 </param>
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210 <when value="none">
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211 </when>
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212 <when value="simple">
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213 <expand macro="simple_identification_params" />
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214 </when>
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215 <when value="advanced">
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216 <expand macro="simple_identification_params" />
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217 <expand macro="advanced_identification_params" />
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218 </when>
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219 </conditional>
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220 </macro>
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221 <macro name="site_quantification_conditional">
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222 <conditional name="site_quantification">
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223 <param name="specify" type="boolean" label="Specify Advanced Site Quantification Parameters" checked="false" />
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224 <when value="false">
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225 </when>
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226 <when value="true">
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227 <param name="site_quant_mode" type="select" label="Site Quantification Mode">
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228 <!-- TODO verify values -->
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229 <option value="0" selected="true">Use least modified peptides</option>
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230 <option value="1">Use largest change</option>
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231 </param>
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232 <param name="use_norm_ratios_for_occupancy" type="boolean" label="Use normalized Ratios for Occupancy" truevalue="true" falsevalue="false" checked="true"/>
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233 </when>
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234 </conditional>
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235 </macro>
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236 <macro name="protein_quantification_conditional">
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237 <conditional name="quantification">
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238 <param name="specify" type="boolean" label="Specify Advanced Protein Quantification Parameters" checked="false" />
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239 <when value="false">
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240 </when>
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241 <when value="true">
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242 <conditional name="restrict">
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243 <param name="restrict_protein_quantification" type="boolean" label="Restrict Protein Quantification" checked="true" help="to unmodified peptides and those with certain modifications."/>
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244 <when value="false">
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245 </when>
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246 <when value="true">
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247 <param name="restrict_modifications" label="Modifications for Quantification" type="select" help="If advanced protein quantification parameters is not selected these default to Oxidation (M) and Actetyl (Protein N-term), but they must be selected (if desired) in this mode." multiple="true">
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248 <expand macro="mod_opts" />
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249 </param>
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250 </when>
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251 </conditional>
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252 <param name="quant_mode" type="select" label="Protein Quantification Mode">
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253 <option value="0">Use all peptides</option>
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254 <option value="1" selected="true">Use razor and unique peptides</option>
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255 <option value="2">Use unique peptides</option>
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256 </param>
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257 <param name="use_counterparts" type="boolean" label="Discard Unmodified Counterpart Peptides." checked="true" truevalue="false" falsevalue="true" />
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258 <param name="min_ratio_count" label="Minimum Ratio Count" value="2" type="integer" />
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259 </when>
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260 </conditional>
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261 </macro>
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262 <macro name="simple_identification_params">
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263 <param name="protein_fdr" label="Protein FDR" value="0.01" type="float" />
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264 <param name="peptide_fdr" label="Peptide FDR" value="0.01" type="float" />
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265 <param name="site_fdr" label="Protein FDR" value="0.01" type="float" />
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266 </macro>
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267 <macro name="advanced_identification_params">
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268 <param name="peptide_pep" label="Max Peptide PEP" value="1" type="float" />
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269 <!-- TODO: Apply site FDR seperately (boolean), Min peptides, Min Score,
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270 min peptide length, min razor + unique peptides, filter labeled aa,
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271 min unique peptides, second peptides (boolean true) -->
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272 </macro>
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273 <macro name="misc_conditional">
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274 <conditional name="misc">
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275 <param name="specify" type="boolean" label="Specify Misc Parameters" checked="false" />
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276 <when value="false">
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277 </when>
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278 <when value="true">
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279 <param name="re_quantify" type="boolean" label="Re-quantify" checked="true" truevalue="true" falsevalue="false" />
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280 <!--
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281 "Keep low-scoring versions of identified peptides" 0 = No, 1 only within parameters groups, 2 = Also between parameter groups.
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282 Match Between Runs: bool
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283 Time window (minutes): 2
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284 Label-free quantification:
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285 LFO min ratio count 2
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286 Fast LFQ
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287 iBAQ
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288 Log fit
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289 -->
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290 </when>
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291 </conditional>
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292 </macro>
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293 </macros>
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294 <inputs>
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295 <conditional name="analysis_type">
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296 <param name="type" type="select" value="single" help="The wrapper has not yet implemented multiple groups with different parameters">
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297 <option value="single">Single Group</option>
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298 <option value="multi_same">Multi-Group Identical Parameters</option>
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299 </param>
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300 <when value="multi_same">
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301 <repeat name="groups">
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302 <expand macro="input_param" />
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303 </repeat>
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304 <expand macro="group_params" />
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305 </when>
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306 <when value="single">
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307 <expand macro="input_param" />
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308 <expand macro="group_params" />
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309 </when>
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310 </conditional>
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311 <param format="fasta" name="database" type="data" label="FASTA Database" help="" />
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312 <expand macro="advanced_sequences_conditional" />
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313 <param name="fixed_modifications" label="Fixed Modifications" type="select" multiple="true">
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314 <expand macro="mod_opts" />
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315 </param>
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316 <expand macro="identification_conditional" />
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317 <expand macro="protein_quantification_conditional" />
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318 <expand macro="site_quantification_conditional" />
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319 <expand macro="misc_conditional" />
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320 </inputs>
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321 <outputs>
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322 <data format="tabular" name="output_protein_groups" label="MaxQuant Protein Groups for ${on_string}"/>
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323 <data format="tabular" name="output_peptides" label="MaxQuant Peptides for ${on_string}"/>
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324 <data format="tabular" name="output_evidence" label="MaxQuant Evidence for ${on_string}"/>
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325 <data format="tabular" name="output_parameters" label="MaxQuant Tabular Parameters for ${on_string}"/>
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326 <data format="tabular" name="output_msms" label="MaxQuant MSMS for ${on_string}"/>
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327 <data format="tabular" name="output_mqpar" label="MaxQuant Parameters XML for ${on_string}"/>
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328 </outputs>
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329 <help>
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330 </help>
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331 </tool>
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