# HG changeset patch
# User drosofff
# Date 1433764557 14400
# Node ID 118834adb4ce0040aed57b7a5334d86bf820b96b

planemo upload for repository https://bitbucket.org/drosofff/gedtools/

diff -r 000000000000 -r 118834adb4ce cap3.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cap3.xml	Mon Jun 08 07:55:57 2015 -0400
@@ -0,0 +1,34 @@
+<tool id="cap3" name="cap3" version="1.0.1">
+<description>Sequence Assembly tool</description>
+    <requirements>
+    	<requirement type="package" version="3">cap3</requirement>
+    </requirements>
+<command>
+cap3 "$inputSequences" > "$cap3stdout";
+                mv "$inputSequences".cap.contigs $contigs;
+                mv "$inputSequences".cap.contigs.qual $contigsqual;
+                mv "$inputSequences".cap.contigs.links $contigslink;
+                mv "$inputSequences".cap.ace $ace;
+                mv "$inputSequences".cap.info $info;
+                mv "$inputSequences".cap.singlets $singlets;
+
+</command>
+
+        <inputs>
+        	<param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" />
+        </inputs>
+
+<outputs>
+        	<data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output"/>
+                <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" />
+                <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="True" />
+                <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="True" />
+                <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="True" />
+                <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="True" />
+                <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" hidden="True" />
+</outputs>
+
+<help>
+
+</help>
+</tool>
diff -r 000000000000 -r 118834adb4ce tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jun 08 07:55:57 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="cap3" version="3">
+      <repository changeset_revision="a472ccd208e2" name="package_cap3_3" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>