diff hicup_digester.xml @ 4:a2f3a4129052 draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3

--- a/hicup_digester.xml	Thu Nov 09 11:15:47 2017 -0500
+++ b/hicup_digester.xml	Fri May 25 17:54:32 2018 -0400
@@ -4,9 +4,7 @@
         <import>hicup_macros.xml</import>
     </macros>
     <expand macro="requirements_hicup" />
-    <expand macro="stdio" />
-
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
         hicup_digester --re1 '$re1' --genome '$genome'
         #if $advanced_options.re2:
             --re2 '$advanced_options.re2'
@@ -14,23 +12,24 @@
         #for $file in $input_files_digest:
             $file
         #end for
-        && mv *Digest_* digester_file.txt
     ]]></command>
     <inputs>
-        <expand macro="digester_input" />
-        <expand macro="re1" />   
+        <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/>
+        <param argument="--genome" type="text" label="Genome name"
+            help="Name of the genome to be digested."/>
+        <expand macro="re1" />
         <section name="advanced_options" title="Advanced options">
             <expand macro="re2" />
         </section>
     </inputs>
     <outputs>
-        <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
+        <data name="digest_file" format="txt" from_work_dir="Digest_*" label="Digester File.txt"/>
     </outputs>
      <tests>
         <test>
-            <param name="input_files_digest" value="chr1.fa"/>
+            <param name="input_files_digest" value="chr21And22FromHg38.fasta"/>
             <param name="re1" value="A^AGCTT"/>
-            <param name="genome" value="human"/>
+            <param name="genome" value="chr21And22FromHg38"/>
             <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
         </test>
     </tests>