diff seqtk_mutfa.xml @ 3:bc7d99f46a5d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d

--- a/seqtk_mutfa.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_mutfa.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,29 +1,32 @@
 <?xml version="1.0"?>
 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
-  <description>point mutate FASTA at specified positions</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk mutfa
-      $in_file $in_snp
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_mutfa.fa"/>
-      <param name="in_snp" value="seqtk_mutfa.snp"/>
-      <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+    <description>point mutate FASTA at specified positions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk mutfa
+'$in_file'
+'$in_snp'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" label="Mutated $in_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_mutfa.fa"/>
+            <param name="in_snp" value="seqtk_mutfa.snp"/>
+            <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
@@ -47,6 +50,6 @@
     GCTAACTGAA
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>