Mercurial > repos > bgruening > hicexplorer_hiccorrelate

annotate hicCorrelate.xml @ 0:fe0243c46b36 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
author bgruening
date Thu, 30 Mar 2017 02:50:08 -0400
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children ae2d7e2dfeef
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fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Computes pairwise correlations between hic matrices data</description>
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3 <macros>
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4 <token name="@BINARY@">hicCorrelate</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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fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 @multiple_input_matrices@
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12 hicCorrelate
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14 --matrices $matrices
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15 --labels $mlabels
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17 #if $method and $method is not None:
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18 --method $method
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19 #end if
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20 $log1p
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22 #if $use_range.select_use_range == "yes_use_range"
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23 --range $range_min:$range_max
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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24 #end if
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26 #if $chromosomes:
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27 --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])#
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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28 #end if
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30 --colorMap $colormap
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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31
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32 --outFileNameHeatmap ./heatmap.png
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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33 --outFileNameScatter ./scatter.png
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34 ]]>
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35 </command>
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36 <inputs>
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37 <expand macro="multiple_input_matrices" />
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38
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39 <param name="method" type="select" label="Correlation method to use" argument="--method" >
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40 <option value="spearman">Spearman</option>
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41 <option selected="true" value="pearson">Pearson</option>
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42 </param>
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43 <param name="log1p" type="boolean" argument="--log1p" truevalue="--log1p" falsevalue=""
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44 label="Use the log1p of the matrix values" help="(--log1p)" />
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45 <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
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46 <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
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47 <option value="no_use_range">No restriction</option>
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48 <option value="yes_use_range">Only consider counts within a range</option>
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49 </param>
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50 <when value="no_use_range"/>
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51 <when value="yes_use_range">
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52 <param name="range_min" type="integer" value="" min="0"/>
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53 <param name="range_max" type="integer" value="" min="0"/>
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54 </when>
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55 </conditional>
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56 <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
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57 <param name="chromosome" type="text"/>
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58 </repeat>
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59
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60 <expand macro="colormap" />
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61
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62 </inputs>
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63 <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
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64 <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
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65 <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
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66 </outputs>
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67 <tests>
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68 <test>
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69 <repeat name="input_files">
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70 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
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71 <param name="mlabel" value="first"/>
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72 </repeat>
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73 <repeat name="input_files">
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74 <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
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75 <param name="mlabel" value="second"/>
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76 </repeat>
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77 <param name="log1p" value="True"/>
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78 <param name="colormap" value="jet"/>
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79 <param name="method" value="spearman"/>
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80 <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
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81 <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85
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86 **What it does**
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87
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88 Computes pairwise correlations between hic matrices data.
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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89 The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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90
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91
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92 ]]></help>
fe0243c46b36 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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93 <expand macro="citations" />
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94 </tool>