# HG changeset patch
# User iuc
# Date 1659704234 0
# Node ID 144e435c648300e7bebb3f06403342a2a2b6c593
# Parent  150ffb616b02ddfa109854e5c335136031f5d115
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit f09c6b7e45ccd61956942b5aab76c0c8ccc0fe03

diff -r 150ffb616b02 -r 144e435c6483 hamronize_summarize.xml
--- a/hamronize_summarize.xml	Tue Jul 05 22:36:27 2022 +0000
+++ b/hamronize_summarize.xml	Fri Aug 05 12:57:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 
+<tool id="hamronize_summarize" name="hamronize: summarize" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description> harmorization reports</description>
     <macros>
         <import>macros.xml</import>
@@ -12,20 +12,19 @@
             #elif $report.is_of_type('json'):
                 #set $ext = 'json'
             #end if
-        ln -s '$report' ./report_${counter}.${ext} &&
+            ln -s '$report' ./report_${counter}.${ext} &&
         #end for
 
         hamronize summarize
         --summary_type $summary_type
-        #if $summary_type == "tsv" 
+        #if $summary_type == "tsv"
             --output output.tsv
         #elif $summary_type == "json"
             --output output.json
-        #else 
+        #else
              --output output.html
         #end if
-        *.tsv
-        *.json
+        ./report_*
     ]]>    </command>
 
     <inputs>
@@ -70,11 +69,12 @@
     </tests>
     <help>
         <![CDATA[
-        **What it does**
-        This tool will take a list of report and create single sorted report in the specified format just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
-
-        **Inputs**
-        A list of hamronize reports
-    ]]>
+            **What it does**
+            This tool will take a list of report and create single sorted report in the specified format
+            just containing the unique entries across input reports. It can handle mixed json and tsv hamronized report formats
+            **Inputs**
+            A list of hamronize reports
+            
+        ]]>
     </help>
 </tool>
diff -r 150ffb616b02 -r 144e435c6483 macros.xml
--- a/macros.xml	Tue Jul 05 22:36:27 2022 +0000
+++ b/macros.xml	Fri Aug 05 12:57:14 2022 +0000
@@ -1,17 +1,17 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.3</token>
     <token name="@PROFILE@">20.05</token>
-    
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">hamronization</requirement>
         </requirements>
     </xml>
-    
+
     <xml name="input_file_name">
         <param name="input_file_name" type="text" label="Input file name" help="Sample name which was scanned with the tool"></param>
     </xml>
-    
+
     <xml name="reference_database_id">
         <param name="reference_database_id" type="text" label="Reference database ID" help="String containing the reference_database_id of this tool"></param>
     </xml>
@@ -23,8 +23,8 @@
     <xml name="analysis_software_version">
         <param name="analysis_software_version" type="text" label="Analysis software version"></param>
     </xml>
-    
+
     <xml name="version_command">
         <version_command>hamronize --version</version_command>
     </xml>
-</macros>
\ No newline at end of file
+</macros>