Mercurial > repos > bgruening > hicexplorer_hicpca

annotate hicPCA.xml @ 2:cf7dbe6a2606 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
author iuc
date Wed, 03 Jan 2018 13:23:45 -0500
parents e3d020b23ad5
children 02c7b035c9f6
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cf7dbe6a2606 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01
iuc
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1 <tool id="hicexplorer_hicpca" name="@BINARY@" version="@WRAPPER_VERSION@.1">
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2 <description>computes the principal components for A / B compartment analysis</description>
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3 <macros>
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4 <token name="@BINARY@">hicPCA</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 detect_errors="exit_code"><![CDATA[
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9
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10 hicPCA --matrix '$matrix_h5_cooler'
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11
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12 --outputFileName pca1.$outputFormat pca2.$outputFormat
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13 --format $outputFormat
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15 && mv pca1.$outputFormat pca1
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16 && mv pca2.$outputFormat pca2
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro='matrix_h5_cooler_macro' />
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22 <param name='outputFormat' type='select' label="Output file format">
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23 <option value='bigwig' selected="true">bigwig</option>
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24 <option value="bedgraph">bedgraph</option>
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25 </param>
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27 </inputs>
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28 <outputs>
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29
2
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30 <data name="pca1" from_work_dir="pca1" format="bigwig">
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31 <filter>outputFormat == 'bigwig'</filter>
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32 <change_format>
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33 <when input="outputFormat" value="bedgraph" format="bedgraph" />
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34 </change_format>
0
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35 </data>
2
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36 <data name="pca2" from_work_dir="pca2" format="bigwig">
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37 <change_format>
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38 <when input="outputFormat" value="bedgraph" format="bedgraph" />
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39 </change_format>
0
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40 </data>
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41
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42
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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_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
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47 <param name="outputFormat" value="bedgraph" />
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48 <output name="pca1" file="pca1.bedgraph" ftype="bedgraph" compare="sim_size"/>
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49 <output name="pca2" file="pca2.bedgraph" ftype="bedgraph" compare="sim_size"/>
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50 </test>
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51 <test>
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52 <param name="matrix_h5_cooler" value="small_test_matrix_50kb_res.h5"/>
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53
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54 <param name="outputFormat" value="bigwig" />
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55 <output name="pca1" file="pca1.bw" ftype="bigwig" compare="sim_size"/>
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56 <output name="pca2" file="pca2.bw" ftype="bigwig" compare="sim_size"/>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 Principal component analysis
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61 ============================
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62 `hicPCA` computes two eigenvector files based on the input matrix for an A / B compartment analysis.
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63
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64 Input
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65 -----
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66 - the matrix to be analysed
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67
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68 Parameters
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69 __________
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70 - Output file format: bigwig or bedgraph
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71
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72 Output
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73 ------
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74 Two files with the first and the second eigenvector.
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75
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76 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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77
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78 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>