# HG changeset patch
# User yating-l
# Date 1469116271 14400
# Node ID b8726891e16fd4f6c2f503f16e86e8f4ebe50874

planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba

diff -r 000000000000 -r b8726891e16f snap
Binary file snap has changed
diff -r 000000000000 -r b8726891e16f snap.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snap.xml	Thu Jul 21 11:51:11 2016 -0400
@@ -0,0 +1,175 @@
+<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="2006-07-28">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        $__tool_directory__/snap
+        #if $settings.advanced == "advanced"
+        $settings.lcmask
+            #if $settings.strand == "true"
+                $settings.strand.onestrand
+            #end if
+        #end if
+        #if $proteins == "-aa":
+        $proteins "$output2"
+        #end if
+        #if $transcripts == "-tx":
+        $transcripts "$output3"
+        #end if
+        $format
+        $organism
+        "$input1" > "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="dna.gz" />
+        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
+            <option value="A.gambiae.hmm">A.gambiae</option>
+            <option value="A.mellifera.hmm">A.mellifera</option>
+            <option value="A.thaliana.hmm">Arabidopsis thaliana</option>
+            <option value="Acanium.hmm">Acanium</option>
+            <option value="At.hmm">Thale</option>
+            <option value="B.malayi.hmm">Brugia</option>
+            <option value="B.mori.hmm">B.mori</option>
+            <option value="C.elegans.hmm">C.elegans</option>
+            <option value="C.intestinalis.hmm">Ciona</option>
+            <option value="Ce.hmm">Ce</option>
+            <option value="D.melanogaster.hmm">Drosophila melanogaster</option>
+            <option value="Dm.hmm">Dm</option>
+            <option value="ixodesA.hmm">ixodesA</option>
+            <option value="ixodesB.hmm">ixodesB</option>
+            <option value="mam39-ro.hmm">mam39-ro</option>
+            <option value="mam39.hmm">mam39</option>
+            <option value="mam46-ro.hmm">mam46-ro</option>
+            <option value="mam46.hmm">mam46</option>
+            <option value="mam54-ro.hmm">mam54-ro</option>
+            <option value="mam54.hmm">mam54</option>
+            <option value="mamiso.hmm">mamiso</option>
+            <option value="minimal.hmm">minimal</option>
+            <option value="Nasonia.hmm">Nasonia</option>
+            <option value="nGASP.hmm">nGASP</option>
+            <option value="nGASPr.hmm">nGASPr</option>
+            <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>
+        </param>
+        <param name="transcripts" type="select" label="Create FASTA file of transcripts">
+            <option value="-tx">Yes</option>
+            <option value="">No</option>
+        </param>
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Specify advanced parameters">
+                <option value="simple" selected="true">No, use program defaults.</option>
+                <option value="advanced">Yes, see full parameter list.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+                <param name="lcmask" type="boolean" label="treat lowercase as N" truevalue="-lcmask" falsevalue="" />
+                <conditional name="strand">
+                    <param name="strand" type="boolean" label="predict on one strand only" />
+                    <when value="true">
+                    <param name="onestrand" type="select" label="Specify which strand to predict">
+                        <option value="-plus">predict on plus strand only.</option>
+                        <option value="-minus">predict on minus strand only.</option>
+                    </param>
+                    </when>
+                    <when value="false">
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </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 ${on_string}: Protein sequence">
+            <filter>proteins == "-aa"</filter>
+        </data>/Users/yating/Desktop/gonramp/snap-wrapper/thale.gff
+        <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
+            <filter>transcripts == "-tx"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="thale.dna.gz"/>
+            <param name="organism" value="At.hmm" />
+            <param name="format" value="-gff" />
+            <output name="output1" file="thale.gff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        The general form of the snap command line is:
+
+    snap <HMM file> <FASTA file> [options]
+
+HMM file:
+
+    The most convenient way to specify the HMM file is by name. This requires
+    that the ZOE environment variable is set. In this case, snap will look
+    for the HMM file in $ZOE/HMM. You may also specify the HMM file by an
+    explicit path. The following are equivalent if $ZOE is in /usr/local:
+
+        snap C.elegans.hmm ...
+        snap /usr/local/Zoe/HMM/C.elegans.hmm ...
+        snap worm ...  # there are a few convenient aliases in $ZOE/HMM
+
+FASTA file:
+
+    If you have several sequences to analyze, it is more efficient to run
+    snap on a concatenated FASTA file rather than separate runs on single
+    sequence files. The seqeuence may be in a compressed format
+
+    If sequences have been masked with lowercase letters, use -lcmask to
+    prevent exons from appearing in masked DNA.
+
+Output:
+
+    Annotation is reported to stdout in a non-standard format (ZFF). You can
+    change to GFF or ACEDB with the -gff or -ace options. Proteins and
+    transcripts are reported to FASTA files with the -aa and -tx options.
+
+External definitions:
+
+    SNAP allows you to adjust the score of any sequence model at any point
+    in a sequence. This behavior is invoked by giving a ZFF file to SNAP:
+
+        snap <hmm> <sequence> -xdef <ZFF file>
+
+    Each feature description uses the 'group' field to issue a command:
+
+        SET     set the score
+        ADJ     adjust the score up or down
+        OK      set non-cannonical scores
+
+     >FOO
+     Acceptor 120 120 + +50 . . . SET  (sets an Acceptor to 50)
+     Donor    212 212 + -20 . . . ADJ  (lowers a Donor by -20)
+     Inter    338 579 +  -2 . . . ADJ  (lowers Inter by -2 in a range)
+     Coding   440 512 -  +3 . . . ADJ  (raises Coding by +3 in a range)
+     Donor    625 638 +  -5 . . . OK   (sets range of odd Donors to -5)
+
+If the output has scrolled off your screen, try 'snap -help | more'
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{renameTODO,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {TODO},
+  url = {http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz},
+}</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r b8726891e16f test-data/thale.dna.gz
Binary file test-data/thale.dna.gz has changed
diff -r 000000000000 -r b8726891e16f test-data/thale.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/thale.gff	Thu Jul 21 11:51:11 2016 -0400
@@ -0,0 +1,22 @@
+At1g01040.0	SNAP	Einit	1007	1954	85.269	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	2024	2137	8.926	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	2234	2444	20.788	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	2523	2917	35.162	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	3006	3225	34.428	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	3307	3479	14.790	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	3563	3685	4.678	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	3774	3934	10.179	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	4025	4258	25.991	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	4344	4506	4.289	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	4581	4763	28.696	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	4854	5015	15.217	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Exon	5100	5195	23.205	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Eterm	5285	5917	45.878	+	.	At1g01040.0-snap.1
+At1g01040.0	SNAP	Einit	6086	6144	6.596	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	6190	6287	22.495	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	6372	6562	17.809	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	6642	6803	16.407	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	6828	7547	69.159	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	7629	7793	40.262	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Exon	7892	8298	46.310	+	.	At1g01040.0-snap.2
+At1g01040.0	SNAP	Eterm	8384	8561	17.079	+	.	At1g01040.0-snap.2
diff -r 000000000000 -r b8726891e16f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 21 11:51:11 2016 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snap" version="2006-07-28">
+        <install version="1.0">
+            <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="set_environment">
+                    <environment_variable name="ZOE" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </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>