diff _hicExport._xml @ 0:d5bf8c60d661 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:21:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/_hicExport._xml	Thu Mar 30 02:21:47 2017 -0400
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+<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: &quot;dekker&quot; and &quot;ren&quot;.
+            The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels.
+            The &quot;ren&quot; 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>
+