# HG changeset patch
# User computational-metabolomics
# Date 1670434300 0
# Node ID 7f958f54468eff8322548b220bc8d3440f7bc47b
# Parent  26b1c61f7b4cf42f3c8aaab771160a41db7640dd
planemo upload for repository https://github.com/ISA-tools/mzml2isa commit 16f55e636c7d9c2be748cb8212184164e57e4b95

diff -r 26b1c61f7b4c -r 7f958f54468e mzml2isa.xml
--- a/mzml2isa.xml	Wed Dec 07 14:54:23 2022 +0000
+++ b/mzml2isa.xml	Wed Dec 07 17:31:40 2022 +0000
@@ -1,18 +1,15 @@
-<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy0">
+<tool id="mzml2isa" name="mzml2isa" version="1.1.1+galaxy1">
     <description>Parser to get meta information from mzML files and create an ISA-Tab structure</description>
-    
     <requirements>
+        <requirement type="package">zip</requirement>
         <requirement type="package" version="1.1.1">mzml2isa</requirement>
     </requirements>
-
     <stdio>
         <exit_code range="1:" />
     </stdio>
-    
     <command detect_errors="exit_code">
     <![CDATA[
 
-
     #if $input.format == "data_collection"
         mkdir "temp"
         &&
@@ -49,7 +46,6 @@
 	 && zip isa.zip i_* a_* s_* && mv isa.zip "$ISA_zip";
     ]]>
     </command>
-
     <inputs>
         <param name="name_of_study" type="text" label="Name study" help="This should not contain any spaces as the name will be used a prefix for ISA-tab file names" />
         <conditional name="input">
@@ -70,22 +66,18 @@
                 </param>
             </when>
         </conditional>
-
         <param optional="true" format="json" name="metadata" type="data" label="Additional user Metadata in json"  help="A user can add additional metadata directory through a json file"/>
-
     </inputs>
     <outputs>
-
-    <data name="ISA_zip" format="zip" label="ISA Zip file"/>
-    <collection type="list" label="Assay files" name="a_files">
-        <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" directory="."  format="tabular"/>
-	</collection>
-	<collection type="list" label="Study files" name="s_files">
-		<discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="." format="tabular"/>
-	</collection>
-	<data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/>
+        <data name="ISA_zip" format="zip" label="ISA Zip file"/>
+        <collection type="list" label="Assay files" name="a_files">
+            <discover_datasets pattern="(?P&lt;designation&gt;a_.+)\.txt" directory="."  format="tabular"/>
+	    </collection>
+	    <collection type="list" label="Study files" name="s_files">
+		    <discover_datasets pattern="(?P&lt;designation&gt;s_.+)\.txt" directory="." format="tabular"/>
+	    </collection>
+	    <data name="i_file" format="tabular" label="Investigation file" from_work_dir="i_Investigation.txt"/>
     </outputs>
-
     <tests>
         <test>
             <param name="name_of_study" value="test" />
@@ -152,8 +144,4 @@
         <citation type="doi">10.1007/s11306-015-0879-3</citation>
         <citation type="doi">10.1038/ng.1054</citation>
     </citations>
-</tool>
-
-
-
-
+</tool>
\ No newline at end of file