Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix
comparison _hicExport._xml @ 0:aa854293da07 draft
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
| author | bgruening |
|---|---|
| date | Sun, 09 Oct 2016 17:35:21 -0400 |
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| children |
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| -1:000000000000 | 0:aa854293da07 |
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| 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: "dekker" and "ren". | |
| 22 The dekker format outputs the whole matrix where the first column and first row are the bin widths and labels. | |
| 23 The "ren" 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 |