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annotate fragpipe.xml @ 3:da9ebef968bd draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit b1b03bb7cd31c1ec806b286d6c9444428b358e15
author galaxyp
date Thu, 12 Sep 2024 08:06:44 +0000
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14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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1 <tool id="fragpipe" name="FragPipe - Academic Research and Education User License (Non-Commercial)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Data analysis for mass spectrometry-based proteomics</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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8 <stdio>
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9 <!-- The error code from individual tools run by FragPipe is not always propogated to the FragPipe process exit code -->
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10 <regex match="exit code: [^0]"
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11 source="stdout"
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12 level="fatal"
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13 description="A FragPipe pipeline process returned non-zero exit code."/>
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14 </stdio>
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16 <version_command>fragpipe --help | grep 'FragPipe v'</version_command>
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18 <!--
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19 FragPipe wrapper command:
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20 - Links input files
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21 - Modifies database path in workflow file
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22 - Runs Philosopher to add decoys and contaminants
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23 - Runs FragPipe, passing paths to MSFragger, Philosopher, Python, and IonQuant
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24 -->
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25 <command detect_errors="exit_code"><![CDATA[
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26 ## Create symlink for workflow output
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27 ln -s $workflow_configfile fp.workflow;
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28
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29 ## The user may opt to only output the workflow to review the parameters. If they haven't selected this option, we prepare and run FragPipe.
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30 #if not $workflow_only
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31 @PREPARE_ENVIRONMENT@
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32 @PREPARE_INPUTS@
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33 @PREPARE_DATABASE@
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34
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35 ## Run FragPipe
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36 '$__tool_directory__/fragpipe'
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37 --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a
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38 --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa
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39 --headless
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40 --threads \${GALAXY_SLOTS:-8}
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41 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
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42 --workflow fp.workflow --manifest fp.manifest
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43 --workdir outputs
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44 --config-msfragger \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar
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45 --config-philosopher \$(which philosopher)
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46 --config-python \$(which python)
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47 --config-ionquant \${env_location}/share/ionquant-*/IonQuant.jar &&
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48
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49 @PREPARE_OUTPUTS@
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50 #end if
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51 ]]></command>
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52
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53 <!-- Config file is a FragPipe workflow file -->
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54 <configfiles>
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55 <expand macro="workflow_configfile" />
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56 </configfiles>
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57
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58 <inputs>
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59 <!-- License agreements -->
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60 <expand macro="license_agreements"/>
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61
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62 <!-- Input scan samples -->
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63 <expand macro="samples"/>
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64
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65 <!-- Searched database -->
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66 <expand macro="fragger_database"/>
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67
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68 <!-- Workflow input, if the user chooses to re-use existing FragPipe workflow. -->
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69 <expand macro="workflow"/>
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70
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71 <!-- Only generate a workflow, don't run FragPipe -->
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72 <param name="workflow_only" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Only generate the workflow output"/>
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73
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74 <param name="output_options" label="Additional outputs" type="select" multiple="true" display="checkboxes" optional="true">
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75 <option value="workflow">FragPipe Workflow</option>
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76 <option value="log">FragPipe Log</option>
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77 <option value="combined_outputs">FragPipe Combined Outputs</option>
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78 <option value="concatenated_outputs">TSV Outputs Concatenated</option>
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79 </param>
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80 </inputs>
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81
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82 <outputs>
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83 <!-- Workflow file used by FragPipe -->
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84 <data name="output_workflow" format="txt" label="${tool.name} on ${on_string}: workflow" from_work_dir="fp.workflow">
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85 <filter>workflow_only or (output_options and 'workflow' in output_options)</filter>
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86 </data>
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87 <!-- FragPipe log -->
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88 <data name="log" format="txt" label="${tool.name} on ${on_string}: log.txt" from_work_dir="outputs/log_*.txt">
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89 <filter>not workflow_only and output_options and 'log' in output_options</filter>
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90 </data>
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91
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92 <!-- Collection outputs comprised of separate results for different experiments -->
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93 <collection name="output_psm" type="list" label="${tool.name} - ${on_string}: psm.tsv" >
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94 <filter>not workflow_only</filter>
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95 <discover_datasets pattern="(?P&lt;designation&gt;.+\.psm.tsv)" ext="tabular" directory="outputs"/>
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96 </collection>
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97 <collection name="output_ion" type="list" label="${tool.name} - ${on_string}: ion.tsv" >
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98 <filter>not workflow_only</filter>
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99 <discover_datasets pattern="(?P&lt;designation&gt;.+\.ion.tsv)" ext="tabular" directory="outputs"/>
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100 </collection>
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101 <collection name="output_peptide" type="list" label="${tool.name} - ${on_string}: peptide.tsv" >
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102 <filter>not workflow_only</filter>
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103 <discover_datasets pattern="(?P&lt;designation&gt;.+\.peptide.tsv)" ext="tabular" directory="outputs"/>
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104 </collection>
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105 <collection name="output_protein" type="list" label="${tool.name} - ${on_string}: protein.tsv" >
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106 <filter>not workflow_only</filter>
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107 <discover_datasets pattern="(?P&lt;designation&gt;.+\.protein.tsv)" ext="tabular" directory="outputs"/>
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108 </collection>
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109
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110 <!-- Combined results from all experimental groups -->
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111 <collection name="combined_outputs" type="list" label="${tool.name} - ${on_string}: Combined Outputs" >
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112 <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter>
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113 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/>
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114 </collection>
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115
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116 <!-- Galaxy-wrapper concatenated results -->
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117 <data name="concat_psm_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv">
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118 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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119 </data>
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120 <data name="concat_ion_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv">
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121 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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122 </data>
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123 <data name="concat_peptide_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv">
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124 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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125 </data>
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126 <data name="concat_protein_tsv" format="tabular" label="${tool.name} on ${on_string}: Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv">
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127 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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128 </data>
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129
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130 <!-- PTM-Shepherd Results -->
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131 <data name="global_profile_tsv" format="tabular" label="${tool.name} on ${on_string}: global.profile.tsv" from_work_dir="outputs/global.profile.tsv">
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132 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter>
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133 </data>
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134 <data name="global_summary_tsv" format="tabular" label="${tool.name} on ${on_string}: global.modsummary.tsv" from_work_dir="outputs/global.modsummary.tsv">
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135 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter>
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136 </data>
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137 <data name="global_diagmine_tsv" format="tabular" label="${tool.name} on ${on_string}: global.diagmine.tsv" from_work_dir="outputs/global.diagmine.tsv">
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138 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter>
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139 </data>
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140
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141 <!--
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142 TMT/iTRAW Results
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143 Only produced by TMT, TRAQ, and SLC workflows
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144 -->
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145 <collection name="tmt_results" type="list" label="${tool.name} - ${on_string}: TMT Results" >
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146 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/>
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147 <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter>
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148 </collection>
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149 </outputs>
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150
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151 <tests>
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152 <test expect_num_outputs="11">
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153 <param name="inputs" value="default/test1.mzML,default/test2.mzML" ftype="mzml"/>
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154 <param name="database_name" value="default/test.fasta" ftype="fasta"/>
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155 <param name="manifest" value="default/test.manifest" ftype="tabular"/>
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156 <param name="workflow_name" value="Default"/>
3
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157 <param name="label_free_quantification_run" value="ionquant"/>
0
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158 <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
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159 <param name="license_agreements" value="true"/>
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160 <output name="concat_psm_tsv" ftype="tabular">
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161 <assert_contents>
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162 <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
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163 <has_text text="sample1"/>
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164 </assert_contents>
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165 </output>
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166 <output name="concat_ion_tsv" ftype="tabular">
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167 <assert_contents>
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168 <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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169 <has_text text="sample1"/>
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170 </assert_contents>
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171 </output>
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172 <output name="concat_peptide_tsv" ftype="tabular">
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173 <assert_contents>
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174 <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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175 <has_text text="sample1"/>
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176 </assert_contents>
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177 </output>
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178 <output name="concat_protein_tsv" ftype="tabular">
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179 <assert_contents>
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180 <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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181 <has_text text="sample1"/>
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182 </assert_contents>
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183 </output>
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184 <output name="output_workflow" ftype="txt" file="default/outputs/workflow.txt" compare="contains">
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185 <assert_contents>
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186 <has_text text="crystalc.run-crystalc=false"/>
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187 </assert_contents>
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188 </output>
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189 <output name="log" ftype="txt">
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190 <assert_contents>
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191 <has_text text="FragPipe version 20.0"/>
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192 </assert_contents>
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193 </output>
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194 <output_collection name="combined_outputs" type="list">
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195 <element name="combined_protein.tsv" ftype="tabular">
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196 <assert_contents>
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197 <has_text text="Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Length&#x9;Organism&#x9;Protein Existence&#x9;Description&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Combined Total Peptides&#x9;Combined Spectral Count&#x9;Combined Unique Spectral Count&#x9;Combined Total Spectral Count&#x9;sample1 Spectral Count&#x9;sample2 Spectral Count&#x9;sample1 Intensity&#x9;sample2 Intensity&#x9;Indistinguishable Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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198 </assert_contents>
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199 </element>
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200 </output_collection>
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201 </test>
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202 <test expect_num_outputs="11">
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203 <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
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204 <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
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205 <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>
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206 <param name="annotation" value="tmt11/test.annotation" ftype="tabular"/>
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207 <param name="workflow_name" value="TMT11"/>
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208 <param name="output_options" value="workflow,log,concatenated_outputs"/>
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209 <param name="license_agreements" value="true"/>
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210 <output name="concat_psm_tsv" ftype="tabular">
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211 <assert_contents>
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212 <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File&#x9;Peptide&#x9;Modified Peptide&#x9;Extended Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Charge&#x9;Retention&#x9;Observed Mass&#x9;Calibrated Observed Mass&#x9;Observed M/Z&#x9;Calibrated Observed M/Z&#x9;Calculated Peptide Mass&#x9;Calculated M/Z&#x9;Delta Mass&#x9;Expectation&#x9;Hyperscore&#x9;Nextscore&#x9;PeptideProphet Probability&#x9;Number of Enzymatic Termini&#x9;Number of Missed Cleavages&#x9;Protein Start&#x9;Protein End&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Purity&#x9;Is Unique&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
213 <has_text text="sample1"/>
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214 </assert_contents>
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215 </output>
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216 <output name="concat_ion_tsv" ftype="tabular">
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217 <assert_contents>
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218 <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;M/Z&#x9;Charge&#x9;Observed Mass&#x9;Probability&#x9;Expectation&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
219 <has_text text="sample1"/>
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220 </assert_contents>
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221 </output>
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222 <output name="concat_peptide_tsv" ftype="tabular">
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223 <assert_contents>
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galaxyp
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224 <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;Next AA&#x9;Peptide Length&#x9;Protein Start&#x9;Protein End&#x9;Charges&#x9;Probability&#x9;Spectral Count&#x9;Intensity&#x9;Assigned Modifications&#x9;Observed Modifications&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Protein Description&#x9;Mapped Genes&#x9;Mapped Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
225 <has_text text="sample1"/>
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226 </assert_contents>
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227 </output>
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228 <output name="concat_protein_tsv" ftype="tabular">
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229 <assert_contents>
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230 <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;Entry Name&#x9;Gene&#x9;Length&#x9;Organism&#x9;Protein Description&#x9;Protein Existence&#x9;Coverage&#x9;Protein Probability&#x9;Top Peptide Probability&#x9;Total Peptides&#x9;Unique Peptides&#x9;Razor Peptides&#x9;Total Spectral Count&#x9;Unique Spectral Count&#x9;Razor Spectral Count&#x9;Total Intensity&#x9;Unique Intensity&#x9;Razor Intensity&#x9;Razor Assigned Modifications&#x9;Razor Observed Modifications&#x9;Indistinguishable Proteins"/>
14785481da2b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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diff changeset
231 <has_text text="sample1"/>
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232 </assert_contents>
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233 </output>
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234 <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains">
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235 <assert_contents>
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236 <has_text text="crystalc.run-crystalc=false"/>
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237 </assert_contents>
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238 </output>
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239 <output name="log" ftype="txt">
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240 <assert_contents>
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241 <has_text text="FragPipe version 20.0"/>
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242 </assert_contents>
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243 </output>
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244 <output_collection name="tmt_results" type="list">
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245 <element name="abundance_gene_MD.tsv" ftype="tabular">
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246 <assert_contents>
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247 <has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
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248 </assert_contents>
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249 </element>
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250 <element name="ratio_gene_MD.tsv" ftype="tabular">
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251 <assert_contents>
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252 <has_text text="Index&#x9;NumberPSM&#x9;ProteinID&#x9;MaxPepProb&#x9;ReferenceIntensity&#x9;sample-01&#x9;sample-02&#x9;sample-03&#x9;sample-04&#x9;sample-05&#x9;sample-06&#x9;sample-07&#x9;sample-08&#x9;sample-09&#x9;sample-10&#x9;Bridge"/>
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253 </assert_contents>
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254 </element>
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255 </output_collection>
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256 </test>
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257 </tests>
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258
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259 <help><![CDATA[
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260 **FragPipe**
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261
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262 FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.
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263 FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.
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264
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265 FragPipe_ runs a user selected analysis workflow_
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266
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267 **License Agreements**
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268
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269 @LICENSE_AGREEMENTS@
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270
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271 .. _FragPipe: https://fragpipe.nesvilab.org
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272 .. _MSFragger: https://msfragger.nesvilab.org
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273 .. _workflow: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_workflows.html
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274
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275 ]]></help>
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276 <expand macro="citations" />
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277 </tool>