Mercurial > repos > earlhaminst > plotheatmap
comparison plotheatmap.xml @ 0:bd8fd161908b draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty
| author | earlhaminst |
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| date | Wed, 12 Jul 2017 14:29:51 -0400 |
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| -1:000000000000 | 0:bd8fd161908b |
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| 1 <tool id="plotheatmap" name="plotHeatmap" version="1.0"> | |
| 2 <description>Plot heatmap</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.34.0">bioconductor-preprocesscore</requirement> | |
| 5 <requirement type="package" version="3.0.1">r-gplots</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 Rscript '$__tool_directory__/script.R' | |
| 9 '$count_matrix' | |
| 10 '$stats_matrix' | |
| 11 $filter.log_fc | |
| 12 $filter.log_cpm | |
| 13 $filter.pvalue | |
| 14 $filter.fdr | |
| 15 $heatmap.cluster_row | |
| 16 $heatmap.cluster_col | |
| 17 $heatmap.hclust_method | |
| 18 $plotparm.col_marg | |
| 19 $plotparm.row_marg | |
| 20 $plotparm.pdf_width | |
| 21 $plotparm.pdf_height | |
| 22 ]]></command> | |
| 23 <inputs> | |
| 24 <param name="count_matrix" type="data" format="tabular" label="Output dataset 'count_matrix' from tool countMatrixForEdger"/> | |
| 25 <param name="stats_matrix" type="data" format="tabular" label="Output dataset 'output' from tool edgeR"/> | |
| 26 <section name="filter" title="Filtering parameters" expanded="true"> | |
| 27 <param name="log_fc" type="float" value="0.5" label="A log FC threshold"/> | |
| 28 <param name="log_cpm" type="float" value="0.5" label="A log CPM threshold"/> | |
| 29 <param name="pvalue" type="float" min="0" max="1" value="0.5" label="A p-value threshold"/> | |
| 30 <param name="fdr" type="float" min="0" max="1" value="0.5" label="An FDR threshold"/> | |
| 31 </section> | |
| 32 <section name="heatmap" title="Heatmap parameters"> | |
| 33 <param name="cluster_row" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Determines if the row dendrogram should be reordered"/> | |
| 34 <param name="cluster_col" type="boolean" truevalue="Yes" falsevalue="No" label="Determines if the column dendrogram should be reordered"/> | |
| 35 <param name="hclust_method" type="select" label="Hierarchical clustering method"> | |
| 36 <option value="ward.D">ward.D</option> | |
| 37 <option value="ward.D2">ward.D2</option> | |
| 38 <option value="single">single</option> | |
| 39 <option value="complete">complete</option> | |
| 40 <option value="average" selected="true">average</option> | |
| 41 <option value="mcquitty">mcquitty</option> | |
| 42 <option value="median">median</option> | |
| 43 <option value="centroid">centroid</option> | |
| 44 </param> | |
| 45 </section> | |
| 46 <section name="plotparm" title="Plot parameters"> | |
| 47 <param name="col_marg" type="float" value="7" label="Margins for column names"/> | |
| 48 <param name="row_marg" type="float" value="8" label="Margins for row names"/> | |
| 49 <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches (pdf width)"/> | |
| 50 <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches (pdf height)"/> | |
| 51 </section> | |
| 52 </inputs> | |
| 53 <outputs> | |
| 54 <data name="haetamappdf" format="pdf" from_work_dir="heatmap.pdf"/> | |
| 55 </outputs> | |
| 56 <tests> | |
| 57 <test> | |
| 58 <param name="count_matrix" value="count.matrix"/> | |
| 59 <param name="stats_matrix" value="stats.data"/> | |
| 60 <param name="log_fc" value="1"/> | |
| 61 <param name="log_cpm" value="2"/> | |
| 62 <param name="pvalue" value="0.05"/> | |
| 63 <param name="fdr" value="0.1"/> | |
| 64 <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size"/> | |
| 65 </test> | |
| 66 </tests> | |
| 67 <help><![CDATA[ | |
| 68 **What it does** | |
| 69 | |
| 70 It takes a list of genes based on set filtering criteria and draws them on heatmap. | |
| 71 | |
| 72 **Example** | |
| 73 | |
| 74 The following filtering options: | |
| 75 A log FC threshold = 0.5 | |
| 76 A log CPM threshold = 0.5 | |
| 77 A p-value threshold = 0.05 | |
| 78 An FDR threshold = 0.1 | |
| 79 mean that you select genes whose values in output table from edgeR are: | |
| 80 * absolute value of log FC is greater than or equal to 0.5 | |
| 81 * log CPM is greater than or equal to 0.5 | |
| 82 * p-value is less than or equal to 0.05 | |
| 83 * FDR is less than or equal to 0.1 | |
| 84 ]]></help> | |
| 85 <citations> | |
| 86 </citations> | |
| 87 </tool> |