Mercurial > repos > iuc > kegg_pathways_completeness
diff kegg_pathways_completeness.xml @ 0:9933e2f91584 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/kegg_pathways_completeness commit 7352c3ea390d3cd3afe19c0af5be59d8cfbaa7cd
| author | iuc |
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| date | Fri, 05 Dec 2025 17:34:32 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kegg_pathways_completeness.xml Fri Dec 05 17:34:32 2025 +0000 @@ -0,0 +1,135 @@ +<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>