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annotate fragpipe_manifest_generator.xml @ 8:da1531027506 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 6413a461059c4a421a7812a08f244c224cde8ee2
author galaxyp
date Fri, 17 Oct 2025 16:22:52 +0000
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8
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1 <tool id="fragpipe_manifest_generator" name="FragPipe Manifest Generator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>
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3 Generate a FragPipe Manifest File (Experimental Design File)
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 <import>msfragger_macros.xml</import>
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9 <token name="@SCAN_DATA_TYPE_REGEX@">(DDA|DDA+|DIA|GPF-DIA|DIA-Quant|DIA-Lib)</token>
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10 <token name="@RUN_GENERATOR@"><![CDATA[
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11 python '$__tool_directory__/generate_manifest.py'
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12
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13 #if $experiment_conditional_element.entry_type == 'consecutive'
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14 --exp-consec
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15 #elif $experiment_conditional_element.entry_type == 'assign_all'
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16 --exp-assign-all '$experiment_conditional_element.experiment'
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17 #elif $experiment_conditional_element.entry_type == 'column'
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18 --exp-col '$experiment_conditional_element.experiment_values'
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19 #end if
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21 #if $bioreplicate_conditional_element.entry_type == 'consecutive'
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22 --bio-consec
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23 #elif $bioreplicate_conditional_element.entry_type == 'assign_all'
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24 --bio-assign-all '$bioreplicate_conditional_element.bioreplicate'
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25 #elif $bioreplicate_conditional_element.entry_type == 'column'
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26 --bio-col '$bioreplicate_conditional_element.bioreplicate_values'
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27 #end if
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28
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29 #if $scan_data_type_conditional_element.entry_type == 'assign_all'
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30 --type-assign-all '$scan_data_type_conditional_element.scan_data_type'
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31 #elif $scan_data_type_conditional_element.entry_type == 'column'
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32 --type-col '$scan_data_type_conditional_element.scan_data_type_values'
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33 #end if
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34
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35 #for $sf in $inputs_element
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36 #set $i_name = $ln_name($sf)
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37 $i_name
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38 #end for
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39 ]]></token>
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40
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41 <xml name="scan_parameters">
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42 <!-- Input Scan Files -->
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43 <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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44
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45 <!-- Experiment input -->
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46 <conditional name="experiment_conditional">
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47 <param name="entry_type" type="select" label="Assign experiments">
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48 <option value="none" selected="true">Leave blank</option>
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49 <option value="consecutive">Assign consecutive integers</option>
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50 <option value="column">Enter column values</option>
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51 <option value="assign_all">Assign to all scan files</option>
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52 </param>
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53 <when value="none"/>
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54 <when value="consecutive"/>
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55 <when value="column">
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56 <param name="experiment_values" type="text" label="Comma-separated experiment numbers">
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57 <validator type="empty_field"/>
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58 </param>
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59 </when>
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60 <when value="assign_all">
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61 <param name="experiment" type="text" label="Experiment">
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62 <validator type="empty_field"/>
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63 </param>
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64 </when>
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65 </conditional>
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66
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67 <!-- Bioreplicate input -->
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68 <conditional name="bioreplicate_conditional">
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69 <param name="entry_type" type="select" label="Assign bioreplicates">
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70 <option value="none" selected="true">Leave blank</option>
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71 <option value="consecutive">Assign consecutive integers</option>
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72 <option value="column">Enter column values</option>
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73 <option value="assign_all">Assign to all scan files</option>
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74 </param>
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75 <when value="none"/>
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76 <when value="consecutive"/>
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77 <when value="column">
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78 <param name="bioreplicate_values" type="text" label="Comma-separated bioreplicate numbers">
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79 <validator type="empty_field"/>
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80 </param>
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81 </when>
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82 <when value="assign_all">
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83 <param name="bioreplicate" type="text" label="Bioreplicate">
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84 <validator type="empty_field"/>
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85 </param>
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86 </when>
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87 </conditional>
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88
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89 <!-- Data type input -->
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90 <conditional name="scan_data_type_conditional">
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91 <param name="entry_type" type="select" label="Assign scan_data_types">
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92 <option value="column">Enter column values</option>
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93 <option value="assign_all" selected="true">Assign to all scan files</option>
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94 </param>
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95 <when value="assign_all">
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96 <param name="scan_data_type" type="select" optional="false" label="Data Type">
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97 <option value="DDA" selected="true">DDA</option>
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98 <option value="DDA+">DDA+</option>
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99 <option value="DIA">DIA</option>
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100 <option value="GPF-DIA">GPF-DIA</option>
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101 <option value="DIA-Quant">DIA-Quant</option>
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102 <option value="DIA-Lib">DIA-Lib</option>
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103 </param>
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104 </when>
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105 <when value="column">
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106 <param name="scan_data_type_values" type="text" optional="false" label="Comma-separated Data Types">
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107 <validator type="regex">^@SCAN_DATA_TYPE_REGEX@(,@SCAN_DATA_TYPE_REGEX)*$</validator>
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108 </param>
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109 </when>
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110 </conditional>
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111 </xml>
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112 </macros>
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113
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114 <requirements>
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115 <requirement type="package" version="3.11">python</requirement>
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116 </requirements>
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117
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118 <command><![CDATA[
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119 @CMD_IMPORTS@
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120
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121 #set $experiment_conditional_element = $experiment_conditional
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122 #set $bioreplicate_conditional_element = $bioreplicate_conditional
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123 #set $scan_data_type_conditional_element = $scan_data_type_conditional
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124 #set $inputs_element = $inputs
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125
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126 @RUN_GENERATOR@
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127
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128 #for $i, $g in enumerate($scan_groups)
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129 #set $experiment_conditional_element = $g.experiment_conditional
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130 #set $bioreplicate_conditional_element = $g.bioreplicate_conditional
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131 #set $scan_data_type_conditional_element = $g.scan_data_type_conditional
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132 #set $inputs_element = $g.inputs
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133
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134 && @RUN_GENERATOR@
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135 #end for
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136 ]]>
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137 </command>
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138
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139 <inputs>
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140 <expand macro="scan_parameters"/>
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141 <repeat name="scan_groups" title="Additional Scan Groups">
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142 <expand macro="scan_parameters"/>
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143 </repeat>
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144 </inputs>
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145
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146 <outputs>
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147 <data name="manifest_file" format="tabular" label="FragPipe Manifest File" from_work_dir="fp.manifest"/>
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148 </outputs>
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149
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150 <tests>
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151 <!-- Test different entry types -->
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152 <test expect_num_outputs="1">
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153 <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/>
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154 <param name="experiment_conditional|entry_type" value="consecutive"/>
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155 <param name="bioreplicate_conditional|entry_type" value="column"/>
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156 <param name="bioreplicate_conditional|bioreplicate_values" value="3,4"/>
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157 <param name="scan_data_type_conditional|entry_type" value="assign_all"/>
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158 <param name="scan_data_type_conditional|scan_data_type" value="DIA"/>
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159 <output name="manifest_file" ftype="tabular" file="manifest-generator/test1.manifest" compare="contains"/>
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160 </test>
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161 <!-- Test scan groups -->
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162 <test expect_num_outputs="1">
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163 <param name="inputs" value="basic-search/test1.mzML" ftype="mzml"/>
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164 <param name="experiment_conditional|entry_type" value="assign_all"/>
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165 <param name="experiment_conditional|experiment" value="1"/>
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166 <param name="bioreplicate_conditional|entry_type" value="assign_all"/>
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167 <param name="bioreplicate_conditional|bioreplicate" value="1"/>
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168 <param name="scan_data_type_conditional|entry_type" value="assign_all"/>
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169 <param name="scan_data_type_conditional|scan_data_type" value="DIA"/>
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170 <repeat name="scan_groups">
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171 <param name="inputs" value="basic-search/test2.mzML" ftype="mzml"/>
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172 <param name="experiment_conditional|entry_type" value="assign_all"/>
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173 <param name="experiment_conditional|experiment" value="2"/>
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174 <param name="bioreplicate_conditional|entry_type" value="assign_all"/>
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175 <param name="bioreplicate_conditional|bioreplicate" value="2"/>
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176 <param name="scan_data_type_conditional|entry_type" value="assign_all"/>
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177 <param name="scan_data_type_conditional|scan_data_type" value="GPF-DIA"/>
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178 </repeat>
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179 <output name="manifest_file" ftype="tabular" file="manifest-generator/test2.manifest" compare="contains"/>
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180 </test>
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181 </tests>
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182 <help>
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183 Generates a *manifest file* that may be used as input for the FragPipe Galaxy tool, or headless FragPipe_.
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184 This file is analagous to an experimental design file.
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185
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186 The tool takes as input a collection of scan files, or multiple collections using the *Insert Additional Scan Groups* parameter, and options for assigning experiment numbers, bioreplicates,
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187 and data types for each file.
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188
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189 Each scan group will have values from three columns applied to it using different methods.
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190
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191 - Assign consecutive integers: The scans will be number consecutively starting with 1.
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192 - Enter column values: The column values for each scan file are entered as a comma-delimited list in the same order as the files.
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193 - Assign to all scan files: A value supplied by the user is applied to all files.
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194
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195 .. _FragPipe: https://fragpipe.nesvilab.org/docs/tutorial_headless.html
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196 </help>
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197 <expand macro="citations" />
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198 </tool>