--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cloudmap.xml	Sat Dec 13 17:20:01 2014 -0500
@@ -0,0 +1,74 @@
+<tool id="cloudmap_prepare" name="Prepare variant data for mapping">
+  <description>with the CloudMap series of tools.</description>
+  <requirements>
+    <requirement type="package" version="0.1.5">mimodd</requirement>
+  </requirements>
+  <version_command>mimodd version -q</version_command>
+  <command>
+    mimodd cloudmap "$ifile" ${run.mode} 
+    
+    #if $str($run.mode) != "EMS":
+        "${run.refsample}"
+    #end if
+    
+    "$sample" -o $ofile
+    
+    #if $seqdict:
+        -s $dictfile
+    #end if
+  </command>
+
+  <inputs>
+    <param name="ifile" type="data" format="vcf" label="vcf input file" />
+    <conditional name="run">
+      <param name="mode" type="select" label="CloudMap analysis to prepare data for">
+        <option value="EMS">EMS Variant Density Mapping</option>
+        <option value="VARIANT">Variant Discovery Mapping</option>
+        <option value="HAWAIIAN">Hawaiian Variant Mapping</option>
+      </param>
+      <when value="EMS">
+        <param name="refsample" type="hidden" value="None" />
+      </when>
+      <when value="VARIANT">
+        <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be EXCLUDED from the analysis" />
+      </when>
+      <when value="HAWAIIAN">
+        <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be INCLUDED in the analysis" />
+      </when>
+    </conditional>
+    <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
+    <param name="seqdict" type="boolean" checked="true" label="Generate species configuration file for CloudMap" />      
+      
+  </inputs>
+
+  <outputs>
+    <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" />
+    <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
+      <filter>seqdict</filter>
+    </data>
+  </outputs>
+
+  <help>
+.. class:: infomark
+
+   **What it does**
+
+The purpose of this tool is to provide compatibility of the MiModD analysis workflow with the external `CloudMap`_ *EMS Variant Density Mapping*, *Variant Discovery Mapping* and *Hawaiian Variant Mapping* tools.
+
+These tools complement MiModD by providing easily interpreted visualizations of mapping-by-sequencing analysis workflows.
+
+The tool converts a VCF file as generated by the *Extract Variant Sites* or *VCF Filter* tools to the format expected by the *CloudMap* series of tools.
+
+Optionally, it also extracts the chromosome names and sizes and reports them in the *CloudMap* *species configuration file* format.
+Such a file is required as input to the current versions of the *CloudMap* *Hawaiian* and *Variant Density* mapping tools, if you are working with a species other than the natively supported ones (i.e., other than *C. elegans* or *A. thaliana*).
+
+To use the output datasets of the tool with *CloudMap*, you only have to upload them to any public Galaxy server that hosts *CloudMap* like, e.g., the main Galaxy server at https://usegalaxy.org .
+
+.. class:: warningmark
+
+   EMS Variant Density Mapping is currently limited to *C. elegans* and other species with six chromosomes on the *CloudMap* side.
+
+.. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
+
+  </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Dec 13 17:20:01 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="mimodd" version="0.1.5">
+      <repository changeset_revision="fbac402764d6" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>