Mercurial > repos > iuc > drhip
diff drhip.xml @ 0:dd2d60b55e0d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d
| author | iuc |
|---|---|
| date | Thu, 04 Dec 2025 15:05:26 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/drhip.xml Thu Dec 04 15:05:26 2025 +0000 @@ -0,0 +1,265 @@ +<tool id="drhip" name="DRHIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Data Reduction for HyPhy with Inference Processing</description> + <macros> + <token name="@TOOL_VERSION@">0.1.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">25.0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">drhip</requirement> + </requirements> + <version_command>drhip --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p hyphy_input + + ## For each method, create directory + link files with pattern: gene.METHOD.json + #if $busted_files + && mkdir -p hyphy_input/BUSTED + #for $file in $busted_files + && ln -s '${file}' 'hyphy_input/BUSTED/${file.element_identifier}.BUSTED.json' + #end for + #end if + + #if $fel_files + && mkdir -p hyphy_input/FEL + #for $file in $fel_files + && ln -s '${file}' 'hyphy_input/FEL/${file.element_identifier}.FEL.json' + #end for + #end if + + #if $meme_files + && mkdir -p hyphy_input/MEME + #for $file in $meme_files + && ln -s '${file}' 'hyphy_input/MEME/${file.element_identifier}.MEME.json' + #end for + #end if + + #if $prime_files + && mkdir -p hyphy_input/PRIME + #for $file in $prime_files + && ln -s '${file}' 'hyphy_input/PRIME/${file.element_identifier}.PRIME.json' + #end for + #end if + + #if $relax_files + && mkdir -p hyphy_input/RELAX + #for $file in $relax_files + && ln -s '${file}' 'hyphy_input/RELAX/${file.element_identifier}.RELAX.json' + #end for + #end if + + #if $contrastfel_files + && mkdir -p hyphy_input/CONTRASTFEL + #for $file in $contrastfel_files + && ln -s '${file}' 'hyphy_input/CONTRASTFEL/${file.element_identifier}.CONTRASTFEL.json' + #end for + #end if + + ## Run DRHIP with tabular output + && drhip + --input hyphy_input + --output output_dir + --tabular + ]]></command> + <inputs> + <param name="busted_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="BUSTED results" + help="HyPhy BUSTED JSON result(s). Element identifier is used as gene name."/> + <param name="fel_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="FEL results" + help="HyPhy FEL JSON result(s). Element identifier is used as gene name."/> + <param name="meme_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="MEME results" + help="HyPhy MEME JSON result(s). Element identifier is used as gene name."/> + <param name="prime_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="PRIME results" + help="HyPhy PRIME JSON result(s). Element identifier is used as gene name."/> + <param name="relax_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="RELAX results" + help="HyPhy RELAX JSON result(s). Required for comparison group analyses. Element identifier is used as gene name."/> + <param name="contrastfel_files" type="data" format="hyphy_results.json" multiple="true" optional="true" + label="Contrast-FEL results" + help="HyPhy Contrast-FEL result(s). Required for comparison group analyses. Element identifier is used as gene name."/> + </inputs> + <outputs> + <data name="combined_summary" format="tabular" from_work_dir="output_dir/combined_summary.tab" + label="${tool.name} on ${on_string}: Combined Summary"/> + <data name="combined_sites" format="tabular" from_work_dir="output_dir/combined_sites.tab" + label="${tool.name} on ${on_string}: Combined Sites"/> + <data name="combined_comparison_summary" format="tabular" from_work_dir="output_dir/combined_comparison_summary.tab" + label="${tool.name} on ${on_string}: Combined Comparison Summary"> + <filter>relax_files or contrastfel_files</filter> + </data> + <data name="combined_comparison_site" format="tabular" from_work_dir="output_dir/combined_comparison_site.tab" + label="${tool.name} on ${on_string}: Combined Comparison Site"> + <filter>relax_files or contrastfel_files</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="busted_files" value="BUSTED/gene1.json" ftype="hyphy_results.json"/> + <param name="fel_files" value="FEL/gene1.json" ftype="hyphy_results.json"/> + <param name="meme_files" value="MEME/gene1.json" ftype="hyphy_results.json"/> + <param name="prime_files" value="PRIME/gene1.json" ftype="hyphy_results.json"/> + <output name="combined_summary" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="BUSTED" /> + <has_text text="gene1.json" /> + <has_text text="pval" /> + <has_text text="omega" /> + <has_n_lines n="2" /> + <has_n_columns n="9"/> + </assert_contents> + </output> + <output name="combined_sites" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="site" /> + <has_text text="gene1.json" /> + <has_text text="fel_selection" /> + <has_text text="meme_marker" /> + <has_text text="prime_marker" /> + <has_n_lines n="101" /> + <has_n_columns n="8"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <param name="busted_files" value="BUSTED/gene2.json" ftype="hyphy_results.json"/> + <param name="fel_files" value="FEL/gene2.json" ftype="hyphy_results.json"/> + <param name="meme_files" value="MEME/gene2.json" ftype="hyphy_results.json"/> + <param name="prime_files" value="PRIME/gene2.json" ftype="hyphy_results.json"/> + <param name="relax_files" value="RELAX/gene2.json" ftype="hyphy_results.json"/> + <param name="contrastfel_files" value="CONTRASTFEL/gene2.json" ftype="hyphy_results.json"/> + <output name="combined_summary" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="BUSTED" /> + <has_text text="RELAX" /> + <has_text text="gene2.json" /> + <has_text text="pval" /> + <has_text text="omega" /> + <has_n_lines n="2" /> + <has_n_columns n="12"/> + </assert_contents> + </output> + <output name="combined_sites" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="site" /> + <has_text text="gene2.json" /> + <has_text text="fel_selection" /> + <has_text text="meme_marker" /> + <has_text text="prime_marker" /> + <has_n_lines n="101" /> + <has_n_columns n="8"/> + </assert_contents> + </output> + <output name="combined_comparison_summary" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="comparison_group" /> + <has_text text="gene2.json" /> + <has_text text="Foreground" /> + <has_text text="Reference" /> + <has_text text="background" /> + <has_n_lines n="4" /> + <has_n_columns n="6"/> + </assert_contents> + </output> + <output name="combined_comparison_site" ftype="tabular"> + <assert_contents> + <has_text text="gene" /> + <has_text text="site" /> + <has_text text="comparison_group" /> + <has_text text="gene2.json" /> + <has_text text="cfel_beta" /> + <has_text text="Foreground" /> + <has_text text="Reference" /> + <has_n_lines n="301" /> + <has_n_columns n="8"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**DRHIP: Data Reduction for HyPhy with Inference Processing** + +Combines results from multiple HyPhy selection analysis methods into unified tabular files. + +----- + +**What it does** + +DRHIP takes JSON outputs from HyPhy selection analysis tools and creates summary tables that combine results across multiple genes and analysis methods. + +----- + +**Inputs** + +DRHIP expects HyPhy JSON result files from one or more of these methods: + +- **BUSTED** – Branch-site test for episodic diversifying selection +- **FEL** – Fixed effects likelihood test for selection +- **MEME** – Mixed effects model of evolution +- **PRIME** – Property-informed models of evolution +- **RELAX** (optional) – Test for relaxation/intensification of selection +- **Contrast-FEL** (optional) – Compare selection between groups + +At least **one method must have at least one JSON input**. Individual method inputs are marked optional so that: + +- You can run DRHIP with any subset of methods (for example, only BUSTED+FEL), and +- If a method fails for some genes but succeeds for others, you can still pass the successful results and DRHIP will report what it can from the available methods. + +You can provide: +- Single datasets +- Multiple datasets selected at once +- Dataset collections (for workflow use); element identifiers are used as gene names. + +----- + +**Outputs** + +**Always generated (if corresponding inputs are provided):** +- **Combined Summary** (`tabular`) – Gene-level statistics across all supplied methods +- **Combined Sites** (`tabular`) – Site-level analysis results across all supplied methods + +**Generated when RELAX or Contrast-FEL results are provided:** +- **Combined Comparison Summary** (`tabular`) – Group-specific statistics +- **Combined Comparison Site** (`tabular`) – Group-specific site analysis + +----- + +**Typical usage patterns** + +- **Per-gene summary without branch-group comparisons:** provide any subset of BUSTED, FEL, MEME, PRIME results. +- **Branch-group comparisons:** provide the main methods plus RELAX and/or Contrast-FEL to obtain comparison summary and site tables. + +----- + +**Workflow tips** + +- Connect HyPhy tool outputs directly to DRHIP inputs. +- Gene names come from collection element names. +- Rename collection elements to control gene names (for example, remove file extensions). +- Works best with dataset mapping over collections. + +----- + +**More information** + +https://github.com/veg/DRHIP + ]]></help> + <citations> + <citation type="bibtex"> +@software{drhip2024, + author = {Callan, Danielle and Verdonk, Hannah and Kosakovsky Pond, Sergei L}, + title = {DRHIP: Data Reduction for HyPhy with Inference Processing}, + year = {2024}, + url = {https://github.com/veg/DRHIP}, + version = {@TOOL_VERSION@} +} + </citation> + </citations> +</tool> \ No newline at end of file