Mercurial > repos > yating-l > snap
changeset 0:b8726891e16f draft
planemo upload commit 0ba99fe246099cc1827f71f2722d253becee64ba
| author | yating-l |
|---|---|
| date | Thu, 21 Jul 2016 11:51:11 -0400 |
| parents | |
| children | e177d8e95666 |
| files | snap snap.xml test-data/thale.dna.gz test-data/thale.gff tool_dependencies.xml |
| diffstat | 5 files changed, 215 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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
--- /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>