diff scHicPlotConsensusMatrices.xml @ 1:259899fbb6ae draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"

--- a/scHicPlotConsensusMatrices.xml	Thu Jan 23 16:02:12 2020 -0500
+++ b/scHicPlotConsensusMatrices.xml	Tue Mar 10 15:09:29 2020 -0400
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         @BINARY@
 
-        --matrix $matrix_mcooler
+        --matrix $matrix_scooler
         #if $chromosomes:
             #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
             --chromosomes $chromosome
@@ -28,7 +28,7 @@
 
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
         <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
         <expand macro="colormap" />
         <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
@@ -41,7 +41,7 @@
         
     </inputs>
     <outputs>
-        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+        <data name='output_plot' from_work_dir='plot' format='png' label='Consensus matrix plot on ${on_string}'>
             <change_format>
                 <when input="image_file_format" value="svg" format="svg" />
                 <when input="image_file_format" value="pdf" format="pdf" />
@@ -50,13 +50,13 @@
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
             <output name="output_plot" file="scHicPlotConsensusMatrices/plot.png" ftype="png" compare="sim_size" delta="35000"/>        
         </test>
          <test>
-            <param name='matrix_mcooler' value='scHicConsensusMatrices/consensus_matrix.mcool' />
+            <param name='matrix_scooler' value='scHicConsensusMatrices/consensus_matrix.scool' />
             <param name="image_file_format" value="png" />
             <param name="dpi" value="300" />
             <param name="chromosomes" value="chr1 chr2" />
@@ -70,7 +70,7 @@
 Plot consensus matrices
 =======================
 
-scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster.
+scHicPlotConsensusMatrices plots the consensus (average) matrix of a cluster. This tool is useful to compare the single cell clusters.
 
 .. image:: $PATH_TO_IMAGES/consensus_svl_spectral.png
    :width: 50%