# HG changeset patch
# User nml
# Date 1493925834 14400
# Node ID 9121e9f3f2857339bdf8f674acb0d74630b98eab

planemo upload

diff -r 000000000000 -r 9121e9f3f285 neptune.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/neptune.xml	Thu May 04 15:23:54 2017 -0400
@@ -0,0 +1,98 @@
+<tool id="neptune" name="Neptune: Signature Discovery" version="1.2.5.1">
+  <description>Neptune identifies genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.</description>
+
+  <requirements>
+    <requirement type="package" version="1.2.5">neptune</requirement>
+  </requirements>
+
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+
+  <command>
+    neptune
+
+      --inclusion
+      #for $i in $inclusion
+        "$i"
+      #end for
+
+      --exclusion
+      #for $i in $exclusion
+        "$i"
+      #end for
+
+      #if $options.select == "advanced"
+
+        #if $options.kmer:
+          --kmer "$options.kmer"
+        #end if
+
+        #if $options.rate:
+          --rate "$options.rate"
+        #end if
+
+        #if $options.exhits:
+          --exhits "$options.exhits"
+        #end if
+
+        #if $options.size:
+          --size "$options.size"
+        #end if
+
+      #end if
+
+      --output results
+
+      --parallelization \${GALAXY_SLOTS:-8}
+
+      --organization 3
+
+  </command>
+
+  <inputs>
+    <param name="inclusion" type="data_collection" collection_type="list" label="Inclusion" help="The inclusion targets in FASTA format." format="fasta"/>
+    <param name="exclusion" type="data_collection" collection_type="list" label="Exclusion" help="The exclusion targets in FASTA format." format="fasta"/>
+
+    <conditional name="options">
+      <param name="select" type="select" label="Options Type">
+        <option value="basic">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+      </when>
+      <when value="advanced">
+        <param name="kmer" type="integer" label="k" help="The size of the k-mers. This value is automatically calculated if left blank." optional="true"/>
+        <param name="size" type="integer" label="Size" help="The minimum size of reported signatures. The default size is 4k." optional="true"/>
+        <param name="rate" type="float" label="Rate" help="The probability of a mutation or error at an arbitrary position. The default value is 0.01." optional="true" value="0.01"/>
+        <param name="exhits" type="integer" label="Minimum Exclusion" help="The minimum number of inclusion targets that must contain a k-mer observed in the reference to begin or continue building candidate signatures. This will be calculated if not specified." optional="true"  value="1"/>
+      </when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="consolidated" from_work_dir="results/consolidated/consolidated.fasta" format="fasta" label="Neptune Signatures: $inclusion.name and $exclusion.name"></data>
+    <data name="receipt" from_work_dir="results/receipt.txt" format="txt" label="Neptune Parameters: $inclusion.name and $exclusion.name"></data>
+  </outputs>
+
+  <tests>
+    <test>
+      <output name="receipt"/>
+    </test>
+  </tests>
+
+  <help>
+Neptune locates genomic signatures using an exact k-mer matching strategy while
+accommodating k-mer mismatches. The software identifies sequences that are
+sufficiently represented within inclusion targets and sufficiently absent from
+exclusion targets. The signature discovery process is accomplished using
+probabilistic models instead of heuristic strategies.
+
+The inclusion and exclusion targets must be FASTA files.
+  </help>
+
+  <citations>
+    <citation type="doi">10.1101/032227</citation>
+  </citations>
+
+</tool>