Mercurial > repos > iuc > schicexplorer_schicconsensusmatrices

diff scHicConsensusMatrices.xml @ 1:eb72d9d13e6a 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 18:48:08 +0000
parents f12c086eee8c
children aa7b43bf5c6b
line wrap: on
line diff
--- a/scHicConsensusMatrices.xml	Thu Jan 23 20:48:48 2020 +0000
+++ b/scHicConsensusMatrices.xml	Tue Mar 10 18:48:08 2020 +0000
@@ -8,10 +8,10 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix '$matrix_mcooler'
+        --matrix '$matrix_scooler'
         --clusters $clusters
 
-        --outFileName consensus_matrix.mcool
+        --outFileName consensus_matrix.scool
 
         --threads @THREADS@
 
@@ -20,19 +20,19 @@
     ]]></command>
     <inputs>
         
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='clusters' type='data' format='txt' label='Cluster file' help='Cluster file created by scHicCluster, scHicClusterCompartments, scHicClusterMinHash or scHicClusterSVL'/>
         
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="consensus_matrix.mcool" format="mcool" label="${tool.name} on ${on_string}: Consensus matrices"/>
+        <data name="outFileName" from_work_dir="consensus_matrix.scool" format="scool" label="${tool.name} on ${on_string}: Consensus matrices"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <param name='clusters' value='scHicConsensusMatrices/cluster_kmeans.txt' />
-            <output name="outFileName" ftype="mcool">
+            <output name="outFileName" ftype="scool">
                 <assert_contents>
                     <has_h5_keys keys='consensus_matrix_cluster_0, 
                                         consensus_matrix_cluster_0/bins, consensus_matrix_cluster_0/bins/chrom, 
@@ -63,7 +63,8 @@
 Consensus matrices
 ==================
 
-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.
+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
+cool file.
 
 For more information about scHiCExplorer please consider our documentation on readthedocs.io_