Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix
diff _hicExport._xml @ 0:9767c021cd58 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
| author | bgruening |
|---|---|
| date | Thu, 30 Mar 2017 02:30:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/_hicExport._xml Thu Mar 30 02:30:47 2017 -0400 @@ -0,0 +1,55 @@ +<tool id="hicExport" name="hicExport" version="1.0"> + <description>saves a HiC Matrix in text format</description> + <macros> + <token name="@BINARY@">hicExport</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ + hicExport + #if $matrix and $matrix is not None: + --matrix $matrix + #end if + --outputFormat $outputFormat + $clearMaskedBins + --outFileName $output + + ]]></command> + <inputs> + <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" /> + <param label="Output format" name="outputFormat" type="select" + help="There are two possibilities: "dekker" and "ren". + The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels. + The "ren" format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)"> + <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option> + <option value="ren">Ren (chrom, bin_star, bin_end, values)</option> + </param> + <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix" + help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" /> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="matrix" value="hicBuildMatrix_result1.npz"/> + <param name="outputFormat" value="dekker"/> + <output name="output" file="hicExport_result1.txt" ftpye="txt"/> + </test> + <test> + <param name="matrix" value="hicBuildMatrix_result1.npz"/> + <param name="outputFormat" value="ren"/> + <param name="clearMaskedBins" value="True"/> + <output name="output" file="hicExport_result2.txt" ftpye="txt"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Saves a HiC Matrix in text format + + ]]></help> + <expand macro="citations" /> +</tool> +