Mercurial > repos > bgruening > hicexplorer_hicplotmatrix

diff hicPlotMatrix.xml @ 8:d398f5373c70 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author bgruening
date Wed, 07 Mar 2018 03:44:12 -0500
parents f93a78bc045e
children 653c6fead9f9
line wrap: on
line diff
--- a/hicPlotMatrix.xml	Wed Feb 21 11:36:08 2018 -0500
+++ b/hicPlotMatrix.xml	Wed Mar 07 03:44:12 2018 -0500
@@ -7,12 +7,9 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        #if str($pca_conditional.pca_type) == 'bedgraph':
-            ln -s $pca_conditional.pca_bedgraph pca.bedgraph &&
-            #set $pca = '--pca pca.bedgraph'
-        #elif str($pca_conditional.pca_type) == 'bigwig':
+        #if str($pca_conditional.pca_type) == 'bigwig':
             ln -s $pca_conditional.pca_bigwig pca.bw &&
-            #set $pca = '--pca pca.bw'
+            #set $pca = '--bigwig pca.bw'
         #elif str($pca_conditional.pca_type) == '':
             #set $pca = ''
         #end if
@@ -100,14 +97,9 @@
         <conditional name="pca_conditional">
             <param name='pca_type' label='Datatype of eigenvector file' type='select'>
                 <option value='' selected="true"></option>
-                <option value='bedgraph'>bedgraph</option>
                 <option value='bigwig'>bigwig</option>
             </param>
             <when value='' />
-            <when value='bedgraph'>
-                <param name='pca_bedgraph' type="data" format="bedgraph" 
-                            label="Eigenvector file"/>
-            </when>
             <when value='bigwig'>
                 <param name='pca_bigwig'  type="data" format="bigwig" 
                             label="Eigenvector file"/>
@@ -151,8 +143,8 @@
             <param name="matrix_h5_cooler" value="pearson_small_50kb.cool"/>
             <param name="perChromosome" value="True"/>
             <conditional name="pca_conditional">
-                <param name="pca_type" value='bedgraph'/>
-                <param name="pca_bedgraph" value="pca1.bedgraph"/>
+                <param name="pca_type" value='bigwig'/>
+                <param name="pca_bigwig" value="pca1.bw"/>
             </conditional>
             <param name='colormap' value='hot'/>
             <param name="image_file_format" value="svg" />
@@ -193,7 +185,7 @@
 - log / log1p of the values: It is recommended to use log1p.
 - Colormaps_ for the heatmap. 
 - vMin / vMax
-- principal component: a bedgraph or bigwig file containing eigenvector information
+- principal component: a bigwig file containing eigenvector information
 
 Output
 ------