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changeset 20:04e57f9ef873 draft

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planemo upload commit 6e3286c6569d531846474dcd6959378af0317ce3-dirty
author yating-l
date Fri, 12 Aug 2016 15:01:58 -0400
parents a7f57cf408e8
children 211c9b3a5c15
files README.md README.rst readme.rst snap.xml test-data/thale.gff3 tool_dependencies.xml
diffstat 6 files changed, 104 insertions(+), 60 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Aug 12 15:01:58 2016 -0400
@@ -0,0 +1,2 @@
+# SNAP
+Galaxy wrapper for SNAP gene prediction tool
--- a/README.rst	Fri Aug 12 12:03:46 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-Galaxy wrapper for SNAP
-========================
-
-This wrapper is copyright 2016-2017 by Yating Liu
-
-This is a wrapper for the gene prediction tool SNAP. SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
-Parser.
-
-Reference
-----------------------
-
-    Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
-
-Installation
------------------------
-
-To install SNAP, please download SNAP from
-
-http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz
-
-and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile
-fine on any Linux/Unix type operating systems.
-The default compiler is gcc. If you have gcc installed, the easiest is to just compile as:
-```
-  make
-```
-
-The ZOE environment variable is used by SNAP to find the HMM files. Set this
-to the directory containing this file. For example, if you unpackaged the tar-ball in /usr/local/snap, set the ZOE environment variable to /usr/local/snap
-
-```
-    setenv ZOE /usr/local/snap # csh, tcsh, etc
-```
-  or
-```
-    export ZOE=/usr/local/snap # sh, bash, etc
-```
-To install the wrapper copy the snap folder in the galaxy tools and modify the $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. For example:
-```
-<tool file="galaxy/tools/myTools/snap/snap.xml" />
-```
-
-
-
-
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Fri Aug 12 15:01:58 2016 -0400
@@ -0,0 +1,46 @@
+Galaxy wrapper for SNAP
+========================
+
+This wrapper is copyright 2016-2017 by Yating Liu
+
+This is a wrapper for the gene prediction tool SNAP. SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
+Parser.
+
+Reference
+----------------------
+
+    Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
+
+Installation
+-----------------------
+
+To install SNAP, please download SNAP from
+
+http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz
+
+and follow the installation instractions. The software is routinely compiled and tested on Mac OS X. It should compile
+fine on any Linux/Unix type operating systems.
+The default compiler is gcc. If you have gcc installed, the easiest is to just compile as:
+```
+  make
+```
+
+The ZOE environment variable is used by SNAP to find the HMM files. Set this
+to the directory containing this file. For example, if you unpackaged the tar-ball in /usr/local/snap, set the ZOE environment variable to /usr/local/snap
+
+```
+    setenv ZOE /usr/local/snap # csh, tcsh, etc
+```
+  or
+```
+    export ZOE=/usr/local/snap # sh, bash, etc
+```
+To install the wrapper copy the snap folder in the galaxy tools and modify the $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy. For example:
+```
+<tool file="galaxy/tools/myTools/snap/snap.xml" />
+```
+
+
+
+
+
--- a/snap.xml	Fri Aug 12 12:03:46 2016 -0400
+++ b/snap.xml	Fri Aug 12 15:01:58 2016 -0400
@@ -1,6 +1,6 @@
-<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="0.1.0">
+<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="1.0">
     <requirements>
-	<requirement type="package" version="0.1.0">snap</requirement>
+        <requirement type="package" version="1.0">snap</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -19,9 +19,12 @@
         #if $transcripts == "-tx":
         $transcripts "$output3"
         #end if
-        $format
+        -gff
         $organism
-        "$input1" > "$output1"
+        from gff2Togff3 import Convertor
+        f = Convertor("$output1", "$output4")
+        f.convert()
+        "$input1" > "$output4"
     ]]></command>
     <inputs>
         <param type="data" name="input1" format="dna.gz" />
@@ -54,10 +57,6 @@
             <option value="O.sativa.hmm">O.sativa</option>
             <option value="Os.hmm">Os</option>
         </param>
-        <param name="format" label="output format setting" type="select" multiple="false" format="text" help="Choose a output format.">
-            <option value="-gff">GFF</option>
-            <option value="-ace">ACE</option>
-        </param>
         <param name="proteins" type="select" label="Create FASTA file of proteins">
             <option value="-aa">Yes</option>
             <option value="">No</option>
@@ -91,13 +90,10 @@
     </inputs>
     <outputs>
         <data name="output1" format="gff" label="${tool.name} on ${on_string}: GTF/GFF">
-            <change_format>
-                <when input="format" value="-ace" format="acedb" />
-            </change_format>
         </data>
         <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
             <filter>proteins == "-aa"</filter>
-        </data>/Users/yating/Desktop/gonramp/snap-wrapper/thale.gff
+        </data>
         <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
             <filter>transcripts == "-tx"</filter>
         </data>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/thale.gff3	Fri Aug 12 15:01:58 2016 -0400
@@ -0,0 +1,27 @@
+##gff-version 3
+At1g01040.0	SNAP	gene	1007	5917	.	+	.	ID=At1g01040.0-snap.1
+At1g01040.0	SNAP	mRNA	1007	5917	.	+	.	ID=mRNA_At1g01040.0-snap.1;Parent=At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	1007	1954	85.269	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2024	2137	8.926	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2234	2444	20.788	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	2523	2917	35.162	+	2	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3006	3225	34.428	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3307	3479	14.790	+	2	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3563	3685	4.678	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	3774	3934	10.179	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4025	4258	25.991	+	1	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4344	4506	4.289	+	1	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4581	4763	28.696	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	4854	5015	15.217	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	5100	5195	23.205	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	CDS	5285	5917	45.878	+	0	Parent=mRNA_At1g01040.0-snap.1
+At1g01040.0	SNAP	gene	6086	8561	.	+	.	ID=At1g01040.0-snap.2
+At1g01040.0	SNAP	mRNA	6086	8561	.	+	.	ID=mRNA_At1g01040.0-snap.2;Parent=At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6086	6144	6.596	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6190	6287	22.495	+	1	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6372	6562	17.809	+	2	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6642	6803	16.407	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	6828	7547	69.159	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	7629	7793	40.262	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	7892	8298	46.310	+	0	Parent=mRNA_At1g01040.0-snap.2
+At1g01040.0	SNAP	CDS	8384	8561	17.079	+	1	Parent=mRNA_At1g01040.0-snap.2
--- a/tool_dependencies.xml	Fri Aug 12 12:03:46 2016 -0400
+++ b/tool_dependencies.xml	Fri Aug 12 15:01:58 2016 -0400
@@ -1,6 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snap" version="0.1.0">
-        <repository changeset_revision="0bc612de916e" name="package_snap_0_1_0" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="snap" version="1.0">
+        <install version="1.0">
+            <actions_group>
+                <actions>
+                    <action type="download_by_url">http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz</action>
+                    <action type="shell_command">make</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                    <action type="set_environment">
+                        <environment_variable name="ZOE" action="set_to">$INSTALL_DIR</environment_variable>
+                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    </action>
+                </actions>
+            </actions_group>
+        </install>
+        <readme>SNAP is a general purpose gene finding program suitable for both eukaryotic
+            and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid
+            Parser.
+        </readme>
     </package>
 </tool_dependency>