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Changeset 2:779a817f6b10 (2017-07-04)

Previous changeset 1:f9ad70461e5e (2017-07-04) Next changeset 3:f8941b34bb96 (2017-07-04)

Commit message:
Uploaded wrapper

added:
wrapper.xml

diff -r f9ad70461e5e -r 779a817f6b10 wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/wrapper.xml Tue Jul 04 06:52:27 2017 -0400

[

b'@@ -0,0 +1,258 @@\n+<tool id="virannot" name="virannot" version="0.7.1">\n+ <description>de novo viral genome annotator</description>\n+ <requirements>\n+ <container type="docker">vimalkvn/virannot</container>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command><![CDATA[\n+python $__tool_directory__/virannot.py\n+--input $input\n+--blastdb $blastdb.fields.path\n+--rfamdb $rfamdb.fields.path\n+--modifiers $modifiers\n+--threads \\${GALAXY_SLOTS:-5}\n+--typedata $typedata_select\n+--gcode $gcode_select\n+--out "default"\n+--minrepeat $minrepeat\n+--maxrepeat $maxrepeat\n+--minspacer $minspacer\n+--maxspacer $maxspacer\n+\n+#if $readlength\n+ --readlength $readlength\n+#end if\n+#if $locus\n+ --locus $locus\n+#end if\n+#if $gffprint\n+ --gff\n+#end if\n+#if str($blastevalue)\n+ --blastevalue $blastevalue\n+#end if\n+#if str($mincontigsize)\n+ --mincontigsize $mincontigsize\n+#end if\n+#if str($idthr)\n+ --idthr $idthr\n+#end if\n+#if str($coverthr)\n+ --coverthr $coverthr\n+#end if\n+#if str($diffid)\n+ --diffid $diffid\n+#end if\n+#if $blastexh\n+ --blastexh\n+#end if\n+#if str($method.use_phmmer) == "yes"\n+--hmmdb $method.hmmdb.fields.path\n+--hmmerevalue $method.hmmerevalue\n+#else:\n+--fast\n+#end if\n+]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="fasta" label="(Viral) contigs to annotate" help="Input file as a FASTA file. It can contain multiple sequences (e.g. metagenomic contigs)" />\n+ <param name="blastdb" type="select" label="BLAST Database" help="BLAST Protein Database that will be used for the protein function prediction">\n+ <options from_data_table="virannot_blastdb">\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n+ </options>\n+ </param>\n+ <param name="rfamdb" type="select" label="RFAM database used for ribosomal RNA prediction">\n+ <options from_data_table="virannot_rfamdb">\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n+ </options>\n+ </param>\n+ <param name="modifiers" type="data" format="txt" label="Metadata of the contigs" help="Modifiers per every FASTA header according to SeqIn (https://www.ncbi.nlm.nih.gov/Sequin/modifiers.html)" />\n+\t<param name="typedata_select" type="select" label="GenBank division (--typedata)">\n+\t <option value="CON" selected="true">Contig</option>\n+\t <option value="PHG">Phages</option>\n+\t <option value="VRL">Eukaryotic/Archaea virus</option>\n+\t <option value="BCT">Prokaryotic chromosome</option>\n+\t</param>\n+\t<param name="gcode_select" type="select" label="Number of GenBank translation table (--gcode)">\n+\t <option value="1">Standard genetic code [Eukaryotic]</option>\n+\t <option value="2">Vertebrate mitochondrial code</option>\n+\t <option value="3">Yeast mitochondrial code</option>\n+\t <option value="4">Mycoplasma/Spiroplasma and Protozoan/mold/coelenterate mitochondrial code</option>\n+\t <option value="5">Invertebrate mitochondrial code</option>\n+\t <option value="6">Ciliate, dasycladacean and hexamita nuclear code</option>\n+\t <option value="9">Echinoderm/flatworm mitochondrial code</option>\n+\t <option value="10">Euplotid nuclear code</option>\n+\t <option value="11" selected="true">Bacteria/Archaea/Phages/Plant plastid</option>\n+\t <option value="12">Alternative yeast nuclear code</option>\n+\t <option value="13">Ascidian mitochondrial code</option>\n+\t <option value="14">Alternative flatworm mitochondrial code</option>\n+\t <option value="16">Chlorophycean mitochondrial code</option>\n+\t <option value="21">Trematode mitochondrial code</option>\n+\t <option value="22">Scedenesmus obliquus mitochondrial code</option>\n+\t <option value="23">Thraustochytrium mitochondrial code</option>\n+\t <option value="'..b'mat="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="default.tbl" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" ftype="fasta" value="rubella.fasta" />\n+ <param name="outputs" value="csv,gbk,fasta,tbl" />\n+ <output name="default_csv" file="default.csv" />\n+ <output name="default_gbk" file="default.gbk" />\n+ <output name="default_fasta" file="default.fasta" />\n+ <output name="default_tbl" file="default.tbl" />\n+ </test>\n+ <test>\n+ <param name="input" ftype="fasta" value="mu.fasta" />\n+ <param name="outputs" value="csv,gbk,fasta,tbl" />\n+ <output name="default_csv" file="default.csv" />\n+ <output name="default_gbk" file="default.gbk" />\n+ <output name="default_fasta" file="default.fasta" />\n+ <output name="default_tbl" file="default.tbl" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**About VirAnnot**\n+\n+VirAnnot_ is a script written in Python 2.7 that annotates viral\n+genomes automatically (using a de novo algorithm) and predict the\n+function of their proteins using BLAST and HMMER.\n+\n+----\n+\n+**About this Galaxy wrapper**\n+\n+*Installation*\n+\n+#. `Docker <https://www.docker.com>`_ should first be installed and\n+ working on the server where this Galaxy instance is setup. The\n+ **galaxy** user should be part of the **docker** group.\n+\n+#. Download or clone the VirAnnot_ Github repository (as a submodule)\n+ in to the ``tools`` directory.\n+\n+#. Update ``config/tool_conf.xml`` like this::\n+\n+ <section id="annotation" name="Annotation">\n+ <tool file="virannot/wrapper.xml" />\n+ </section>\n+\n+#. Update ``config/tool_data_table_conf.xml`` to add location of loc\n+ files::\n+\n+ \n+ <table name="virannot_blastdb" comment_char="#">\n+ <columns>value, dbkey, name, path</columns>\n+ <file path="tool-data/virannot_blastdb.loc" />\n+ </table>\n+ <table name="virannot_rfamdb" comment_char="#">\n+ <columns>value, dbkey, name, path</columns>\n+ <file path="tool-data/virannot_rfamdb.loc" />\n+ </table>\n+ <table name="virannot_hmmdb" comment_char="#">\n+ <columns>value, dbkey, name, path</columns>\n+ <file path="tool-data/virannot_hmmdb.loc" />\n+ </table>\n+\n+#. Copy ``.loc`` files from ``virannot/tool-data`` to\n+ ``galaxy/tool-data`` and update the database paths within those\n+ files.\n+\n+#. Restart Galaxy.\n+ \n+----\n+\n+**Output files**\n+\n+VirAnnot creates the following output files:\n+\n+* tbl - Table file with all protein information.\n+* gbk - GenBank format file with annotations.\n+* fasta - FASTA format file for GenBank submission\n+* csv - Table file for GenBank submission.\n+* gff - GFF3 format file (if option is selected)\n+\n+----\n+\n+**License and citation**\n+\n+VirAnnot_ and this Galaxy wrapper - `GPLv3 <https://www.gnu.org/copyleft/gpl.html>`_.\n+\n+\n+Galaxy\n+\n+- Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. "Galaxy: a\n+ comprehensive approach for supporting accessible, reproducible, and\n+ transparent computational research in the life sciences." \n+ Genome Biol. 2010 Aug 25;11(8):R86.\n+\n+- Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M,\n+ Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for\n+ experimentalists". Current Protocols in Molecular Biology. \n+ 2010 Jan; Chapter 19:Unit 19.10.1-21.\n+\n+- Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y,\n+ Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy:\n+ a platform for interactive large-scale genome analysis." \n+ Genome Research. 2005 Oct; 15(10):1451-5.\n+\n+You can use this tool only if you agree to the license terms of: `virannot`_.\n+\n+.. _VirAnnot: https://github.com/EGTortuero/virannot\n+\n+]]></help>\n+\n+</tool>\n'