diff seqtk_comp.xml @ 3:bc7d99f46a5d draft

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

--- a/seqtk_comp.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_comp.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,33 +1,33 @@
 <?xml version="1.0"?>
 <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
-  <description>get the nucleotide composition of FASTA/Q</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk comp
+    <description>get the nucleotide composition of FASTA/Q</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk comp
 #if $in_bed:
--r $in_bed
+    -r '$in_bed'
 #end if
-
-$in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
-
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
-      <output name="default" file="seqtk_comp.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/>
+    </inputs>
+    <outputs>
+        <data name="default" format="tabular" label="Nucleotide composition of $in_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
+            <output name="default" file="seqtk_comp.out" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Reports composition of fasta/fastq sequences. For an example sequence like
@@ -46,8 +46,7 @@
     test0      11     4  2  2  2  0  0  1  0    0   0   0
     ambig_ref  15     1  2  3  4  0  4  1  4    0   0   0
 
-
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>