diff transtermhp.xml @ 3:1a1ec22a7e28 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d

--- a/transtermhp.xml	Fri Oct 09 09:40:48 2015 -0400
+++ b/transtermhp.xml	Wed Jun 07 07:53:53 2017 -0400
@@ -1,27 +1,26 @@
-<?xml version="1.0"?>
-<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0">
-  <description>finds rho-independent transcription terminators in bacterial genomes</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[
+<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1">
+    <description>finds rho-independent transcription terminators in bacterial genomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
 #if $reference_genome.source == 'history':
-    ln -s $reference_genome.genome_fasta genomeref.fa &&
+    ln -s '$reference_genome.genome_fasta' genomeref.fa &&
 #end if
 
-python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT
+python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP
 
 #if $reference_genome.source == 'cached':
-    "${reference_genome.fasta_indexes.fields.path}"
+    '${reference_genome.fasta_indexes.fields.path}'
 #elif $reference_genome.source == 'history':
     genomeref.fa
 #end if
 
-$input_gff3
-
-> $output]]></command>
+'$input_gff3'
+> '$output'
+    ]]></command>
     <inputs>
       <conditional name="reference_genome">
         <param name="source" type="select" label="Reference Genome">
@@ -54,19 +53,19 @@
         This is a TODO item that would be nice to get around to eventually
         (perhaps when a user demands it.)
         -->
-  </inputs>
-  <outputs>
-    <data format="gff3" name="output"/>
-  </outputs>
-  <tests>
-      <test>
-          <param name="source" value="history" />
-          <param name="genome_fasta" value="sequence.fasta" />
-          <param name="input_gff3" value="sequence.gff3" />
-          <output name="output" file="sequence.gff3.out" />
-      </test>
-  </tests>
-  <help><![CDATA[
+    </inputs>
+    <outputs>
+        <data format="gff3" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="history" />
+            <param name="genome_fasta" value="sequence.fasta" />
+            <param name="input_gff3" value="sequence.gff3" />
+            <output name="output" file="sequence.gff3.out" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Finds rho-independent transcription terminators in bacterial genomes.