changeset 0:9a0d14f0f249 draft default tip

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author iracooke
date Sat, 14 Jun 2014 18:09:19 -0400
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files README README.md proteindb_from_gff3.xml repository_dependencies.xml
diffstat 4 files changed, 56 insertions(+), 0 deletions(-) [+]
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+++ b/README	Sat Jun 14 18:09:19 2014 -0400
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+Create protein database from gff3 including encoding genome coordinates into the fasta header
+
+Requirements:
+This package uses protk which must be installed separately. 
+
+For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sat Jun 14 18:09:19 2014 -0400
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+# Create protein database from gff3 including encoding genome coordinates into the fasta header
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteindb_from_gff3.xml	Sat Jun 14 18:09:19 2014 -0400
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+<tool id="proteindb_from_gff3" name="Extract proteins from gff3" version="1.0.1">
+	<requirements>
+	    <requirement type="package" version="1.3">protk</requirement>
+   </requirements>
+
+	<description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
+
+	<command>
+		augustus_to_proteindb.rb $gff_file -o $output $coords
+	</command>
+
+
+
+
+	<stdio>
+		<exit_code range="1:"   level="fatal"   description="Failure" />
+	</stdio>
+
+	<inputs>	
+		<param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
+		<param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
+	</inputs>
+
+	<outputs>
+		<data format="fasta" name="output" />
+	</outputs>
+
+
+  <help>
+
+**What it does**
+
+Extract proteins from gff3 and encode genomic coordinates in the fasta header.
+Currently this only works with gff3 generated using the Augustus gene finder
+
+----
+
+**References**
+
+
+  </help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Sat Jun 14 18:09:19 2014 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Proteomics datatypes">
+    <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="http://toolshed.g2.bx.psu.edu" />
+ </repositories>