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annotate fragpipe.xml @ 8:012191b79fda 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 16:22:03 +0000
parents b4f6df8fa89b
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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="24.2">
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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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15 <version_command>
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16 fragpipe --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@ --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@ --help | grep 'FragPipe v'
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17 </version_command>
0
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19 <!--
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20 FragPipe wrapper command:
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21 - Links input files
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22 - Modifies database path in workflow file
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23 - Runs Philosopher to add decoys and contaminants
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24 - Runs FragPipe, passing paths to MSFragger, Philosopher, Python, and IonQuant
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25 -->
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26 <command detect_errors="exit_code"><![CDATA[
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27 ## Create symlink for workflow output
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28 ln -s $workflow_configfile fp.workflow;
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29
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30 ## 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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31 #if not $workflow_only
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32 @PREPARE_ENVIRONMENT@
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33 @PREPARE_INPUTS@
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34 @PREPARE_DATABASE@
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35
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36 mkdir tools &&
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37 ln -s \${env_location}/share/diatracer-*/diaTracer-*/diaTracer-*.jar tools/ &&
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38 ln -s \${env_location}/share/ionquant-*/IonQuant-*/IonQuant-*.jar tools/ &&
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39 ln -s \${env_location}/share/msfragger-*/MSFragger-*/MSFragger-*.jar tools/ &&
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40 ln -s \${env_location}/share/msfragger-*/MSFragger-*/ext tools/ &&
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41
0
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42 ## Run FragPipe
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43 '$__tool_directory__/fragpipe'
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44 --msfragger_key @MSFRAGGER_ACADEMIC_USE_KEY@
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45 --ionquant_key @IONQUANT_ACADEMIC_USE_KEY@
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46 --diatracer_key @DIATRACER_ACADEMIC_USE_KEY@
0
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47 --headless
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48 --threads \${GALAXY_SLOTS:-8}
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49 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
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50 --workflow fp.workflow --manifest fp.manifest
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51 --workdir outputs
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52 --config-tools-folder tools
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53 --config-python \$(which python) &&
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54
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55 @PREPARE_OUTPUTS@
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56 #end if
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57 ]]></command>
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58
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59 <!-- Config file is a FragPipe workflow file -->
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60 <configfiles>
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61 <expand macro="workflow_configfile" />
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62 </configfiles>
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63
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64 <inputs>
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65 <!-- License agreements -->
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66 <expand macro="license_agreements"/>
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67
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68 <!-- Input scan samples -->
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69 <expand macro="samples"/>
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70
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71 <!-- Searched database -->
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72 <expand macro="fragger_database"/>
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73
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74 <!-- Workflow input, if the user chooses to re-use existing FragPipe workflow. -->
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75 <expand macro="workflow"/>
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76
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77 <!-- Only generate a workflow, don't run FragPipe -->
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78 <param name="workflow_only" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Only generate the workflow output"/>
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79
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80 <param name="output_options" label="Additional outputs" type="select" multiple="true" display="checkboxes" optional="true">
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81 <option value="workflow">FragPipe Workflow</option>
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82 <option value="log">FragPipe Log</option>
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83 <option value="combined_outputs">FragPipe Combined Outputs</option>
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84 <option value="concatenated_outputs">TSV Outputs Concatenated</option>
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85 <option value="individual_outputs">Individual Experiment Outputs</option>
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86 </param>
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87 </inputs>
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88
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89 <outputs>
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90 <!-- Workflow file used by FragPipe -->
7
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91 <data name="output_workflow" format="txt" label="FragPipe workflow" from_work_dir="fp.workflow">
0
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92 <filter>workflow_only or (output_options and 'workflow' in output_options)</filter>
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93 </data>
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94 <!-- FragPipe log -->
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95 <data name="log" format="txt" label="FragPipe log.txt" from_work_dir="outputs/log_*.txt">
0
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96 <filter>not workflow_only and output_options and 'log' in output_options</filter>
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97 </data>
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98
7
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99 <!-- DIA-NN Quant -->
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100 <data name="diaquant_msstats_csv" format="csv" label="FragPipe DIA-NN Quant msstats.csv" from_work_dir="outputs/dia-quant-output/msstats.csv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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101 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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102 </data>
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103 <data name="diaquant_msstats_ptm_csv" format="csv" label="FragPipe DIA-NN Quant msstats_ptm.csv" from_work_dir="outputs/dia-quant-output/msstats_ptm.csv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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104 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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105 </data>
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106 <data name="diaquant_report_tsv_speclib" format="txt" label="FragPipe DIA-NN Quant report-tsv.speclib" from_work_dir="outputs/dia-quant-output/report-tsv.speclib">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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107 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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108 </data>
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109 <data name="diaquant_report_gg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.gg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.gg_matrix.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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110 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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111 </data>
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112 <data name="diaquant_report_log_txt" format="txt" label="FragPipe DIA-NN Quant report.log.txt" from_work_dir="outputs/dia-quant-output/report.log.txt">
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113 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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114 </data>
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115 <data name="diaquant_report_pg_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pg_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pg_matrix.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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116 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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117 </data>
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118 <data name="diaquant_report_pr_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.pr_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.pr_matrix.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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119 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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120 </data>
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121 <data name="diaquant_report_stats_tsv" format="tsv" label="FragPipe DIA-NN Quant report.stats.tsv" from_work_dir="outputs/dia-quant-output/report.stats.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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122 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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123 </data>
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124 <data name="diaquant_report_tsv" format="tsv" label="FragPipe DIA-NN Quant report.tsv" from_work_dir="outputs/dia-quant-output/report.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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125 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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126 </data>
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127 <data name="diaquant_report_unique_genes_matrix_tsv" format="tsv" label="FragPipe DIA-NN Quant report.unique_genes_matrix.tsv" from_work_dir="outputs/dia-quant-output/report.unique_genes_matrix.tsv">
b4f6df8fa89b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
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128 <filter>(not workflow_only) and ('DIA_SpecLib_Quant' in wf['workflow_name'])</filter>
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129 </data>
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130
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131
0
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132 <!-- Collection outputs comprised of separate results for different experiments -->
7
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133 <collection name="output_psm" type="list" label="FragPipe psm.tsv" >
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134 <filter>not workflow_only and 'individual_outputs' in output_options</filter>
0
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135 <discover_datasets pattern="(?P&lt;designation&gt;.+\.psm.tsv)" ext="tabular" directory="outputs"/>
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136 </collection>
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137 <collection name="output_ion" type="list" label="FragPipe ion.tsv" >
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138 <filter>not workflow_only and 'individual_outputs' in output_options</filter>
0
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139 <discover_datasets pattern="(?P&lt;designation&gt;.+\.ion.tsv)" ext="tabular" directory="outputs"/>
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140 </collection>
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141 <collection name="output_peptide" type="list" label="FragPipe peptide.tsv" >
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142 <filter>not workflow_only and 'individual_outputs' in output_options</filter>
0
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143 <discover_datasets pattern="(?P&lt;designation&gt;.+\.peptide.tsv)" ext="tabular" directory="outputs"/>
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144 </collection>
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145 <collection name="output_protein" type="list" label="FragPipe protein.tsv" >
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146 <filter>not workflow_only and 'individual_outputs' in output_options</filter>
0
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147 <discover_datasets pattern="(?P&lt;designation&gt;.+\.protein.tsv)" ext="tabular" directory="outputs"/>
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148 </collection>
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149
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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150 <!-- Combined results from all experimental groups -->
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151 <collection name="combined_outputs" type="list" label="FragPipe Combined Outputs" >
0
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152 <filter>not workflow_only and output_options and 'combined_outputs' in output_options</filter>
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153 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/combined_outputs"/>
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154 </collection>
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155
41990c43f371 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 905cc2be18669cffe9ac6c46fcd08b6857a67f4f
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156 <!-- Galaxy-wrapper concatenated results -->
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157 <data name="concat_psm_tsv" format="tabular" label="FragPipe Concatenated psm.tsv" from_work_dir="outputs/concat_psm.tsv">
0
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158 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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159 </data>
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160 <data name="concat_ion_tsv" format="tabular" label="FragPipe Concatenated ion.tsv" from_work_dir="outputs/concat_ion.tsv">
0
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161 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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162 </data>
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163 <data name="concat_peptide_tsv" format="tabular" label="FragPipe Concatenated peptide.tsv" from_work_dir="outputs/concat_peptide.tsv">
0
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164 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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165 </data>
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166 <data name="concat_protein_tsv" format="tabular" label="FragPipe Concatenated protein.tsv" from_work_dir="outputs/concat_protein.tsv">
0
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167 <filter>not workflow_only and 'concatenated_outputs' in output_options</filter>
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168 </data>
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169
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170 <!-- PTM-Shepherd Results -->
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171 <data name="global_profile_tsv" format="tabular" label="FragPipe global.profile.tsv" from_work_dir="outputs/ptm-shepherd-output/global.profile.tsv">
0
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172 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter>
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173 </data>
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174 <data name="global_summary_tsv" format="tabular" label="FragPipe global.modsummary.tsv" from_work_dir="outputs/ptm-shepherd-output/global.modsummary.tsv">
0
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175 <filter>(not workflow_only) and ('Open' in wf['workflow_name'])</filter>
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176 </data>
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177
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178 <!--
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179 TMT/iTRAW Results
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180 Only produced by TMT, TRAQ, and SLC workflows
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181 -->
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182 <collection name="tmt_results" type="list" label="FragPipe TMT Results" >
0
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183 <discover_datasets pattern="__designation__" ext="tabular" directory="outputs/tmt-report"/>
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184 <filter>(not workflow_only) and ('TMT' in wf['workflow_name'])</filter>
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185 </collection>
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186 </outputs>
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187
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188 <tests>
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189 <test expect_num_outputs="11">
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190 <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/>
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191 <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/>
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192 <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/>
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193 <param name="wf|workflow_name" value="Basic-Search"/>
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194 <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs,individual_outputs"/>
0
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195 <param name="license_agreements" value="true"/>
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196 <param name="wf|validation|validation_tab|psm_validation|run_psm_validation" value="percolator"/>
0
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197 <output name="concat_psm_tsv" ftype="tabular">
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198 <assert_contents>
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199 <has_text text="Experiment&#x9;Spectrum&#x9;Spectrum File"/>
0
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200 <has_text text="sample1"/>
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201 <has_text text="sample2"/>
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202 </assert_contents>
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203 </output>
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204 <output name="concat_ion_tsv" ftype="tabular">
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205 <assert_contents>
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206 <has_text text="Experiment&#x9;Peptide Sequence&#x9;Modified Sequence"/>
0
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207 <has_text text="sample1"/>
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208 <has_text text="sample2"/>
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209 </assert_contents>
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210 </output>
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211 <output name="concat_peptide_tsv" ftype="tabular">
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212 <assert_contents>
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213 <has_text text="Experiment&#x9;Peptide&#x9;Prev AA&#x9;"/>
0
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214 <has_text text="sample1"/>
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215 <has_text text="sample2"/>
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216 </assert_contents>
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217 </output>
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218 <output name="concat_protein_tsv" ftype="tabular">
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219 <assert_contents>
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220 <has_text text="Experiment&#x9;Protein&#x9;Protein ID&#x9;"/>
0
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221 <has_text text="sample1"/>
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222 <has_text text="sample2"/>
0
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223 </assert_contents>
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224 </output>
7
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225 <output name="output_workflow" ftype="txt" file="basic-search/outputs/workflow.txt" compare="contains"/>
0
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226 <output name="log" ftype="txt">
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227 <assert_contents>
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228 <has_text text="FragPipe version 23.0"/>
0
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229 </assert_contents>
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230 </output>
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231 <output_collection name="combined_outputs" type="list">
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232 <element name="combined_protein.tsv" ftype="tabular">
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233 <assert_contents>
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234 <has_text text="Protein&#x9;Protein ID&#x9;Entry Name"/>
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235 </assert_contents>
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236 </element>
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237 </output_collection>
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238 </test>
7
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239 <test expect_num_outputs="7">
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240 <param name="inputs" value="basic-search/test1.mzML,basic-search/test2.mzML" ftype="mzml"/>
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241 <param name="database_name" value="basic-search/test.fasta" ftype="fasta"/>
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242 <param name="manifest" value="basic-search/test.manifest" ftype="tabular"/>
6
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243 <param name="wf|workflow_name" value="Nonspecific-HLA"/>
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244 <param name="output_options" value="workflow,log,combined_outputs,concatenated_outputs"/>
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245 <param name="license_agreements" value="true"/>
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246 <output name="output_workflow" ftype="txt" file="nonspecific-hla/outputs/workflow.txt" compare="contains"/>
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247 <output name="concat_protein_tsv" ftype="tabular">
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248 <assert_contents>
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249 <has_text text="sample1"/>
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250 <!-- Check for match from decoy_and_contam option -->
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251 <has_text text="sp|P01375|TNFA_HUMAN"/>
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252 </assert_contents>
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253 </output>
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254 </test>
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255 <test expect_num_outputs="1">
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256 <param name="inputs" value="tmt11/test1.mzML,tmt11/test2.mzML" ftype="mzml"/>
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257 <param name="database_name" value="tmt11/test.fasta" ftype="fasta"/>
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258 <param name="manifest" value="tmt11/test.manifest" ftype="tabular"/>
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259 <param name="wf|annotation" value="tmt11/test.annotation" ftype="tabular"/>
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260 <param name="wf|workflow_name" value="TMT11"/>
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261 <param name="output_options" value="workflow"/>
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262 <param name="license_agreements" value="true"/>
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263 <param name="workflow_only" value="true"/>
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264 <output name="output_workflow" ftype="txt" file="tmt11/outputs/workflow.txt" compare="contains"/>
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265 </test>
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266 </tests>
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267
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268 <help><![CDATA[
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269 **FragPipe**
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270
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271 FragPipe_ is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data.
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272 FragPipe uses MSFragger_ - an ultrafast proteomic search engine suitable for both conventional and “open” (wide precursor mass tolerance) peptide identification.
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273
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274 Each FragPipe job is configured around a user-selected FragPipe _workflow.
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275 Blank optional parameters in the Galaxy tool will default to the settings in the selected FragPipe workflow file.
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276
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277 **License Agreements**
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278
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279 @LICENSE_AGREEMENTS@
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280
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281 .. _FragPipe: https://fragpipe.nesvilab.org
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282 .. _MSFragger: https://msfragger.nesvilab.org
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283 .. _workflow: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_workflows.html
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284
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285 ]]></help>
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286 <expand macro="citations" />
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287 </tool>