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| author | iuc |
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| date | Fri, 05 Dec 2025 17:34:32 +0000 |
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<tool id="kegg_pathways_completeness" name="Calculate KEGG Pathways completeness" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Compute KEGG pathway/module completeness from KOs or per-contig annotation</description> <macros> <token name="@TOOL_VERSION@">1.3.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">24.0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">kegg-pathways-completeness</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ give_completeness #if $usr_ref_files.definitions --definitions '$usr_ref_files.definitions' #end if #if $usr_ref_files.names --names '$usr_ref_files.names' #end if #if $usr_ref_files.classes --classes '$usr_ref_files.classes' #end if $w $p #if str($input_type.select_input_type) == "input_list" -l '$l' #else -i '$i' #if $input_type.m $input_type.m && mv summary.kegg_contigs* $kegg_contig_table #end if #end if && mv summary.kegg_pathways* $kegg_pathways_table ]]></command> <inputs> <conditional name="input_type"> <param name="select_input_type" type="select" label="Select input format" help="See the Help section below for examples"> <option value="input_file">Table with one pathway per row</option> <option value="input_list">Text file containing a comma-separated list of KOs</option> </param> <when value="input_file"> <param argument="-i" label="Input file" type="data" format="tabular"/> <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Creates per-contig summary table"/> </when> <when value="input_list"> <param argument="-l" label="Input list" type="data" format="txt"/> </when> </conditional> <section name="usr_ref_files" title="Custom Reference Files" help="Optionally, provide your own KEGG reference files instead of using the default KEGG database"> <param argument="--definitions" label="All modules definitions" type="data" format="txt" optional="true"/> <param argument="--names" label="Modules names" type="data" format="txt" optional="true"/> <param argument="--classes" label="Modules classes" type="data" format="txt" optional="true"/> </section> <param argument="-w" type="boolean" truevalue="-w" falsevalue="" checked="false" label="Add weights for each KO in output"/> <param argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Create images with pathways completeness"/> </inputs> <outputs> <data name="kegg_pathways_table" format="tsv" label="${tool.name} on ${on_string}: KEGG pathway completness table"/> <data name="kegg_contig_table" format="tsv" label="${tool.name} on ${on_string}: KEGG contig pathway completness table"> <filter>input_type['select_input_type'] == "input_file" and input_type['m'] is True</filter> </data> <collection name="pathway_plots" type="list" label="${tool.name} on ${on_string}: Pathway plots" format="png"> <filter>p is True</filter> <discover_datasets pattern="(?P<designation>.+).png" directory="pathways_plots"/> </collection> </outputs> <tests> <test expect_num_outputs="3"> <conditional name="input_type"> <param name="select_input_type" value="input_file"/> <param name="i" value="input_file.tabular"/> <param name="m" value="true"/> </conditional> <section name="usr_ref_files"> <param name="definitions" value="all_pathways.txt"/> <param name="names" value="all_pathways_names.txt"/> <param name="classes" value="all_pathways_class.txt"/> </section> <param name="w" value="true"/> <param name="p" value="true"/> <output name="kegg_pathways_table" file="summary.kegg_pathways.with_wreights.tsv" ftype="tsv"/> <output name="kegg_pathways_table" file="summary.kegg_contigs.with_weights.tsv" ftype="tsv"/> <output_collection name="pathway_plots" type="list" count="9"> <element name="M00003" file="pathway_plots/M00003.png" ftype="png"/> <element name="M00017" file="pathway_plots/M00017.png" ftype="png"/> <element name="M00018" file="pathway_plots/M00018.png" ftype="png"/> <element name="M00082" file="pathway_plots/M00082.png" ftype="png"/> <element name="M00165" file="pathway_plots/M00165.png" ftype="png"/> <element name="M00873" file="pathway_plots/M00873.png" ftype="png"/> <element name="M00874" file="pathway_plots/M00874.png" ftype="png"/> <element name="M00885" file="pathway_plots/M00885.png" ftype="png"/> <element name="M00886" file="pathway_plots/M00886.png" ftype="png"/> </output_collection> </test> <test expect_num_outputs="1"> <conditional name="input_type"> <param name="select_input_type" value="input_list"/> <param name="l" value="input_list.txt"/> </conditional> <output name="kegg_pathways_table" file="summary.kegg_pathways.tsv" ftype="tsv"/> </test> </tests> <help><![CDATA[ **Compute KEGG pathway/module completeness from KOs or per-contig annotations** Input formats: * Example input file (tabular, one pathway per row): contig1 K00812 K12252 K00003 contig1 K02990 K19302 K00645 * Example KO list file (comma-separated): K00001,K00002,K00123,K00942 **Tool license**: `Apache License 2.0 <https://raw.githubusercontent.com/EBI-Metagenomics/kegg-pathways-completeness-tool/refs/heads/master/LICENSE>`_ ]]></help> <creator> <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053"/> </creator> <citations> <citation type="bibtex"> @misc{kegg-pathways-completeness, author = {{EBI‐Metagenomics}}, title = {kegg-pathways-completeness-tool}, howpublished = {\url{https://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool}}, note = {Accessed: 2025-12-05}, year = {2024} } </citation> </citations> </tool>