diff scHicInfo.xml @ 1:09f8be8a6e76 draft

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

--- a/scHicInfo.xml	Thu Jan 23 16:02:54 2020 -0500
+++ b/scHicInfo.xml	Tue Mar 10 15:10:08 2020 -0400
@@ -1,27 +1,24 @@
 <tool id="schicexplorer_schicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
-    <description>information about a single-cell mcool matrix</description>
+    <description>information about a single-cell scool matrix</description>
     <macros>
         <token name="@BINARY@">scHicInfo</token>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-    #import re
-        #set mcoolFile = @ESCAPE_IDENTIFIER_MCOOL@
-        ln -s '$matrix_mcooler' '$mcoolFile' &&
+    <command detect_errors="exit_code"><![CDATA[ 
         @BINARY@
-        --matrix $mcoolFile
+        --matrix '$matrix_scooler'
         >> matrices_info.txt
     ]]></command>
     <inputs>
-        <expand macro="matrix_mcooler_macro"/>
+        <expand macro="matrix_scooler_macro"/>
    </inputs>
     <outputs>
         <data name="outFileName" from_work_dir="matrices_info.txt" format="txt" label="${tool.name} on ${on_string}: Matrix Info"/>
     </outputs>
     <tests>
         <test>
-            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='matrix_scooler' value='test_matrix.scool' />
             <output name="outFileName" file="scHicInfo/matrices_info.txt" ftype="txt" compare="sim_size" delta="4000"/>
         </test>
     </tests>
@@ -30,11 +27,11 @@
 Consensus matrices
 ==================
 
-scHicInfo gives information about the single-cell Hi-C mcool file. For example: 
+scHicInfo gives information about the provided single-cell Hi-C scool file. For example: 
 
 .. code-block::
 
-    Filename: nagano2017_raw.mcool
+    Filename: nagano2017_raw.scool
     Contains 3882 single-cell matrices
     The information stored via cooler.info of the first cell is: