Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

annotate hicPlotDistVsCounts.xml @ 0:4aa65933bc9b draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
author bgruening
date Sun, 09 Oct 2016 17:35:43 -0400
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4aa65933bc9b planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 6a4d8b48a6504eacbb9ed7228f77117fa759286d-dirty
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1 <tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>distance vs HiC counts plot per chromosome</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotDistVsCounts</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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12 ln -s '$matrix' input_matrix.npz.h5 &&
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14 @BINARY@
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16 --matrix input_matrix.npz.h5
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17 $skipDiagonal
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18 --plotFile plot.png
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19 #if $plotTitle and $plotTitle is not None:
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20 --plotTitle '$plotTitle'
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21 #end if
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23 ## special: --chromosomeExclude is optional, but if given needs at least one argument
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24 #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ])
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25 #if $chromosomeExclude:
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26 --chromosomeExclude $chroms
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27 #end if
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/>
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33
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34 <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
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35 <param argument="--plotTitle" type="text" optional="true" label="Plot title"/>
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36 <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude">
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37 <param argument="--chromosomeExclude" type="text" value="" />
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38 </repeat>
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39
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40 </inputs>
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41 <outputs>
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42 <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
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47 <param name="skipDiagonal" value="False"/>
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48 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
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49 </test>
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50 <test>
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51 <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
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52 <param name="skipDiagonal" value="False"/>
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53 <param name="plotTitle" value="Excluded chrUextra"/>
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54 <repeat name="chromosomeExclude">
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55 <param name="chromosomeExclude" value="chrUextra"/>
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56 </repeat>
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57 <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61
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62 **What it does**
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63
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64 This program makes a distance vs. hi-c counts plot per chromosome.
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67 ]]></help>
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68 <expand macro="citations" />
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69 </tool>
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