Mercurial > repos > bgruening > hicexplorer_hicfindtads

diff hicFindTADs.xml @ 5:db2cc9e1ff76 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 80462804e4fd7deafbcf8e8c5283cc7a98fa7dd5
author bgruening
date Sat, 30 Dec 2017 09:39:05 -0500
parents 8b60271e7e54
children b05f292d220c
line wrap: on
line diff
--- a/hicFindTADs.xml	Sat Dec 16 16:32:17 2017 -0500
+++ b/hicFindTADs.xml	Sat Dec 30 09:39:05 2017 -0500
@@ -6,9 +6,8 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        
         hicFindTADs
-                --matrix '$matrix'
+                --matrix '$matrix_h5_cooler'
                
                 --delta $delta
 
@@ -32,7 +31,8 @@
                 --outPrefix galaxy_tad_prefix
     ]]></command>
     <inputs>
-        <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/>
+        <expand macro='matrix_h5_cooler_macro' />
+
         <param argument="--minDepth" type="integer" value="40000"
                 label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
                 help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
@@ -93,7 +93,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrix" value="small_test_matrix.h5" ftype="h5" />
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+
             <param name="minDepth" value="60000"/>
             <param name="maxDepth" value="180000"/>
             <param name="step" value="20000"/>
@@ -125,7 +126,7 @@
 [Source_].
 
 .. image:: $PATH_TO_IMAGES/z-score.svg
-   :width: 150
+   :width: 100
    
 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_