Mercurial > repos > iuc > schicexplorer_schicconsensusmatrices

annotate scHicConsensusMatrices.xml @ 1:18bdb745b787 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
author iuc
date Tue, 10 Mar 2020 15:06:59 -0400
parents 49e3fe550e7e
children 33b1c99cc709
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1 <tool id="schicexplorer_schicconsensusmatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>creates per cluster one average matrix</description>
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3 <macros>
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4 <token name="@BINARY@">scHicConsensusMatrices</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 @BINARY@
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10
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11 --matrix '$matrix_scooler'
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12 --clusters $clusters
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14 --outFileName consensus_matrix.scool
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16 --threads @THREADS@
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20 ]]></command>
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21 <inputs>
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22
1
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23 <expand macro="matrix_scooler_macro"/>
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24 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
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25
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26 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
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27 </inputs>
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28 <outputs>
1
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29 <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name='matrix_scooler' value='test_matrix.scool' />
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34 <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
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35 <output name="outFileName" ftype="scool">
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36 <assert_contents>
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37 <has_h5_keys keys='consensus_matrix_cluster_0,
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38 consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom,
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39 consensus_matrix_cluster_0/bins/end, consensus_matrix_cluster_0/bins/start,
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40 consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length,
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41 consensus_matrix_cluster_0/chroms/name, consensus_matrix_cluster_0/indexes,
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42 consensus_matrix_cluster_0/indexes/bin1_offset, consensus_matrix_cluster_0/indexes/chrom_offset,
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43 consensus_matrix_cluster_0/pixels, consensus_matrix_cluster_0/pixels/bin1_id,
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44 consensus_matrix_cluster_0/pixels/bin2_id, consensus_matrix_cluster_0/pixels/count,
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45 consensus_matrix_cluster_1, consensus_matrix_cluster_1/bins, consensus_matrix_cluster_1/bins/chrom,
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46 consensus_matrix_cluster_1/bins/end, consensus_matrix_cluster_1/bins/start, consensus_matrix_cluster_1/chroms,
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47 consensus_matrix_cluster_1/chroms/length, consensus_matrix_cluster_1/chroms/name, consensus_matrix_cluster_1/indexes,
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48 consensus_matrix_cluster_1/indexes/bin1_offset, consensus_matrix_cluster_1/indexes/chrom_offset,
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49 consensus_matrix_cluster_1/pixels, consensus_matrix_cluster_1/pixels/bin1_id, consensus_matrix_cluster_1/pixels/bin2_id,
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50 consensus_matrix_cluster_1/pixels/count, consensus_matrix_cluster_2, consensus_matrix_cluster_2/bins,
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51 consensus_matrix_cluster_2/bins/chrom, consensus_matrix_cluster_2/bins/end, consensus_matrix_cluster_2/bins/start,
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52 consensus_matrix_cluster_2/chroms, consensus_matrix_cluster_2/chroms/length, consensus_matrix_cluster_2/chroms/name,
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53 consensus_matrix_cluster_2/indexes, consensus_matrix_cluster_2/indexes/bin1_offset, consensus_matrix_cluster_2/indexes/chrom_offset,
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54 consensus_matrix_cluster_2/pixels, consensus_matrix_cluster_2/pixels/bin1_id, consensus_matrix_cluster_2/pixels/bin2_id,
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55 consensus_matrix_cluster_2/pixels/count'/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59
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60 </tests>
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61 <help><![CDATA[
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62
49e3fe550e7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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63 Consensus matrices
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64 ==================
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65
1
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66 scHicConsensusMatrices creates one consensus matrix for each cluster based on the clustered samples. The consensus matrices are normalized to an equal read coverage level and are all stored in one s
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67 cool file.
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68
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69 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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70
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71 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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72 ]]></help>
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73 <expand macro="citations" />
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74
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75 </tool>