diff seqtk_comp.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_comp.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,52 @@
+<?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
+#if $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[
+**What it does**
+
+Reports composition of fasta/fastq sequences. For an example sequence like
+
+::
+    >test0
+    ACTGACTGAA
+    >ambig_ref
+    ACGTCGTGTTVHDBN
+
+The seqtk tool will report:
+
+::
+
+    #chr       length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
+    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>
+</tool>