comparison _hicExport._xml @ 0:5e0a39c5bcf6 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:59:24 -0400
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-1:000000000000 0:5e0a39c5bcf6
1 <tool id="hicExport" name="hicExport" version="1.0">
2 <description>saves a HiC Matrix in text format</description>
3 <macros>
4 <token name="@BINARY@">hicExport</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command><![CDATA[
9 hicExport
10 #if $matrix and $matrix is not None:
11 --matrix $matrix
12 #end if
13 --outputFormat $outputFormat
14 $clearMaskedBins
15 --outFileName $output
16
17 ]]></command>
18 <inputs>
19 <param label="Matrix to use" name="matrix" type="data" help="(--matrix)" />
20 <param label="Output format" name="outputFormat" type="select"
21 help="There are two possibilities: &quot;dekker&quot; and &quot;ren&quot;.
22 The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels.
23 The &quot;ren&quot; format is a list of tuples of the form chrom, bin_star, bin_end, values. (--outputFormat)">
24 <option selected="true" value="dekker">Dekker (first column and first rows are labels)</option>
25 <option value="ren">Ren (chrom, bin_star, bin_end, values)</option>
26 </param>
27 <param name="clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" label="If set, masked bins are removed from the matrix"
28 help="Masked bins are those that do not have any values, mainly because they are repetitive regions of the genome (--clearMaskedBins)" />
29 </inputs>
30 <outputs>
31 <data format="txt" name="output"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="matrix" value="hicBuildMatrix_result1.npz"/>
36 <param name="outputFormat" value="dekker"/>
37 <output name="output" file="hicExport_result1.txt" ftpye="txt"/>
38 </test>
39 <test>
40 <param name="matrix" value="hicBuildMatrix_result1.npz"/>
41 <param name="outputFormat" value="ren"/>
42 <param name="clearMaskedBins" value="True"/>
43 <output name="output" file="hicExport_result2.txt" ftpye="txt"/>
44 </test>
45 </tests>
46 <help><![CDATA[
47
48 **What it does**
49
50 Saves a HiC Matrix in text format
51
52 ]]></help>
53 <expand macro="citations" />
54 </tool>
55