Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

diff macros.xml @ 5:3bc1425f9000 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:26:27 -0500
parents 652fdcbff650
children 30d427846764
line wrap: on
line diff
--- a/macros.xml	Sat Dec 16 16:32:57 2017 -0500
+++ b/macros.xml	Sat Dec 30 09:26:27 2017 -0500
@@ -1,6 +1,6 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">1.8.1</token>
+    <token name="@WRAPPER_VERSION@">2.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">hicexplorer</requirement>
@@ -11,7 +11,7 @@
 
     <xml name="citations">
         <citations>
-            <citation type="doi">10.5281/zenodo.159780</citation>
+            <citation type="doi">10.5281/zenodo.1123667</citation>
             <yield />
         </citations>
     </xml>
@@ -166,7 +166,7 @@
 
     <xml name="multiple_input_matrices">
         <repeat name="input_files" title="HiC Matrix files" min="2">
-            <param name="matrix" type="data" format="h5"
+            <param name="matrix" type="data" format="h5,cool"
                 label="HiC Matrix file"
                 help=""/>
             <param name="mlabel" type="text" size="30" optional="true" value=""
@@ -179,8 +179,8 @@
         #set $matrices = []
         #set $mlabels = []
         #for $counter, $i in enumerate($input_files):
-            ln -s $i.matrix #echo str($counter)+'.npz.h5'#;
-            #silent $matrices.append( '%s.npz.h5' % $counter )
+            ln -s $i.matrix #echo str($counter)+'_matrix'#;
+            #silent $matrices.append( '%s_matrix' % $counter )
 
             #if str($i.mlabel.value) != "":
                 #set $mlabels += ['"%s"' % ($i.mlabel.value)]
@@ -299,7 +299,15 @@
     <xml name="pseudocount">
         <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
     </xml>
-
+    <xml name='matrix_h5_cooler_macro'>
+    <param name='matrix_h5_cooler'  type="data" format="h5,cool" 
+                            label="Matrix to compute on."/>
+       
+    </xml>
+    <xml name='matrix_h5_cooler_multiple_macro'>
+        <param name='matrix_h5_cooler_multiple'  type="data" format="h5,cool" 
+                            label="Matrix to compute on." multiple="True"/>
+    </xml>
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -525,7 +533,7 @@
     </xml>
 
     <xml name="track_input_h5_macro">
-        <param name="track_input_h5" type="data" format="h5" label="Track file h5 format"/>
+        <param name="track_input_h5" type="data" format="h5, cool" label="Track file h5 or cool format"/>
     </xml>
     <xml name="track_input_bed_macro">
         <param name="track_input_bed" type="data" format="bed" label="Track file bed format"/>