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view hierarchical_clustering_heatmap.xml @ 1:2e7d47c0b027 draft
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author | malex |
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date | Mon, 08 Mar 2021 22:04:06 +0000 |
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children | caba07f41453 |
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<tool id="secimtools_hierarchical_clustering_heatmap" name="Hierarchical Clustering Heatmap" version="@WRAPPER_VERSION@"> <description>- Calculate means per group and plot a heatmap.</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ hierarchical_clustering_heatmap.py --input $input --design $design --uniqID $uniqID #if $dendogram --dendogram #end if --labels $labels --fig $fig ]]></command> <inputs> <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/> <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/> <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/> <param name="dendogram" type="boolean" value="False" label="Add dendogram on heatmap" help="Select 'Yes' to print a dendogram over the heatmap."/> <param name="labels" type="select" label="Select to remove labels from plots" multiple="true" display="checkboxes"> <option value="x">X-axis labels</option> <option value="y">Y-axis labels</option> </param> </inputs> <outputs> <data format="pdf" name="fig" label="${tool.name} on ${on_string}"/> </outputs> <tests> <test> <param name="input" value="ST000006_data.tsv"/> <param name="design" value="ST000006_design.tsv"/> <param name="uniqID" value="Retention_Index" /> <param name="dendogram" value="True" /> <param name="labels" value="x,y" /> <output name="fig" file="ST000006_hierarchical_clustering_heatmap_figure.pdf" compare="sim_size" delta="10000" /> </test> </tests> <help><![CDATA[ @TIP_AND_WARNING@ **Tool Description** This tool generates a hierarchical cluster heatmap from a wide format dataset. An option to add a hierarchical clustering dendrogram on the top of the heatmap figure is included along with an option to removal plot labels. **NOTE:** This script works best with log transformed data that contains no missing data. -------------------------------------------------------------------------------- **Input** - Two input datasets are required. @WIDE@ **NOTE:** The sample IDs must match the sample IDs in the Design File (below). Extra columns will automatically be ignored. @METADATA@ **In addition to your datasets, you need to provide:** **Unique Feature ID** - The column name in your wide dataset that contains the unique IDs for your features. In our example dataset you would input *Compound*. -------------------------------------------------------------------------------- **Output** A PDF file with a hierarchical cluster heatmap of the data ]]></help> <expand macro="citations"/> </tool>