Mercurial > repos > iuc > schicexplorer_schicconsensusmatrices

comparison 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
comparison
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0:49e3fe550e7e 1:18bdb745b787
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @BINARY@ 9 @BINARY@
10 10
11 --matrix '$matrix_mcooler' 11 --matrix '$matrix_scooler'
12 --clusters $clusters 12 --clusters $clusters
13 13
14 --outFileName consensus_matrix.mcool 14 --outFileName consensus_matrix.scool
15 15
16 --threads @THREADS@ 16 --threads @THREADS@
17 17
18 18
19 19
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 22
23 <expand macro="matrix_mcooler_macro"/> 23 <expand macro="matrix_scooler_macro"/>
24 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/> 24 <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
25 25
26 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/> 26 <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
27 </inputs> 27 </inputs>
28 <outputs> 28 <outputs>
29 <data name="outFileName" from_work_dir="consensus_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: Consensus matrices"/> 29 <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33 <param name='matrix_mcooler' value='test_matrix.mcool' /> 33 <param name='matrix_scooler' value='test_matrix.scool' />
34 <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' /> 34 <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
35 <output name="outFileName" ftype="mcool"> 35 <output name="outFileName" ftype="scool">
36 <assert_contents> 36 <assert_contents>
37 <has_h5_keys keys='consensus_matrix_cluster_0, 37 <has_h5_keys keys='consensus_matrix_cluster_0,
38 consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom, 38 consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom,
39 consensus_matrix_cluster_0/bins/end, consensus_matrix_cluster_0/bins/start, 39 consensus_matrix_cluster_0/bins/end, consensus_matrix_cluster_0/bins/start,
40 consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length, 40 consensus_matrix_cluster_0/chroms, consensus_matrix_cluster_0/chroms/length,
61 <help><![CDATA[ 61 <help><![CDATA[
62 62
63 Consensus matrices 63 Consensus matrices
64 ================== 64 ==================
65 65
66 scHicConsensusMatrices creates based on the clustered samples one consensus matrix for each cluster. The consensus matrices are normalized to an equal read coverage level and are stored all in one mcool matrix. 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
67 cool file.
67 68
68 For more information about scHiCExplorer please consider our documentation on readthedocs.io_ 69 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
69 70
70 .. _readthedocs.io: http://schicexplorer.readthedocs.io/ 71 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
71 ]]></help> 72 ]]></help>