diff seqtk_mutfa.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_mutfa.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,51 @@
+<?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[
+**What it does**
+
+the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
+
+::
+
+    # Input fasta
+    >test0
+    ACTGACTGAA
+
+    # Input SNP file
+    test0 1 . G
+    test0 4 . A
+
+This will effect the desired mutations in the output file
+
+::
+
+    # Output result
+    >test0
+    GCTAACTGAA
+
+@ATTRIBUTION@
+]]></help>
+</tool>