diff snippy-core.xml @ 18:bcb74072d3a6 draft

Added snippy-core tool

--- a/snippy-core.xml	Wed Jun 08 23:46:47 2016 -0400
+++ b/snippy-core.xml	Thu Jun 09 03:55:50 2016 -0400
@@ -1,31 +1,66 @@
 <tool id="snippy-core" name="snippy-core" version="0.1.0">
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command><![CDATA[
-        TODO: Fill in command template.
+
+  <requirements>
+      <requirement type="package" version="3.0">snippy</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" />
+  </stdio>
+
+    <command interpreter=perl><![CDATA[
+
+        snippy_core_wrapper.pl
+        $is_reference
+        --mincov $mincov
+        --indirs '${" ".join(map(str, $indirs))}'
+
     ]]></command>
+
     <inputs>
+      <param name="indirs" type="data" multiple="true" format="bgzip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
+      <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
+      <param name="mincov" type="float" value="10.0" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
     </inputs>
+
     <outputs>
+      <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln" />
+      <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab" />
+      <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt" />
     </outputs>
+
     <help><![CDATA[
-        Synopsis:
+Synopsis:
   Combine multiple Snippy folders into a core SNP alignment
+
 Usage:
   ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...
+
 Options:
+
   --help!         This help.
+
   --quiet!        No output to stderr (default '0').
+
   --verbose!      Verbose output (default '0').
+
   --inprefix=s    Preferred input prefix of Snippy files (default 'snps').
+
   --prefix=s      Output file prefix (default 'core').
+
   --noref!        Exclude reference (default '0').
+
   --mincov=i      Minimum depth of coverage to consider core (default '10').
+
   --aformat=s     Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').
 
     ]]></help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file
+
+  <citations>
+    <citation type="bibtex">@UNPUBLISHED{Seemann2013,
+      author = "Seemann T",
+      title = "snippy: fast bacterial variant calling from NGS reads",
+      year = "2015",
+      note = "https://github.com/tseemann/snippy"}</citation>
+  </citations>
+
+</tool>