| Next changeset 1:df7738595640 (2017-02-06) |
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Commit message:
Imported from capsule None |
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added:
datatypes_conf.xml diamond.xml diamond_makedb.xml repository_dependencies.xml tool-data/diamond_database.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 98037ef3d2a9 datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="diamond_database" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="False"/> + </registration> +</datatypes> |
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| diff -r 000000000000 -r 98037ef3d2a9 diamond.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diamond.xml Sun Feb 08 10:05:26 2015 -0500 |
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| b'@@ -0,0 +1,180 @@\n+<tool id="bg_diamond" name="Diamond" version="0.1.6.0">\n+ <description>alignment tool for short sequences against a protein database</description>\n+ <requirements>\n+ <requirement type="package" version="0.6.13">diamond</requirement>\n+ </requirements>\n+ <command>\n+<![CDATA[\n+\n+ #if $ref_db_source.db_source == "history":\n+ ln -s $ref_db_source.reference_database ./database.dmnd\n+ #else:\n+ ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd\n+ #end if\n+\n+ &&\n+\n+ diamond\n+ $method.method_select\n+ --threads "\\${GALAXY_SLOTS:-12}"\n+ --db ./database\n+ --query $query\n+ --out $blast_output\n+ ##--sam $sam_output\n+ --compress 0\n+ --tmpdir ./\n+\n+ #if str($hit_filter.hit_filter_select) == \'max\':\n+ --max-target-seqs $hit_filter.max\n+ #else:\n+ --top $hit_filter.percentage\n+ #end if\n+\n+ #if str($filter_score.filter_score_select) == \'evalue\':\n+ --evalue $filter_score.evalue\n+ #else:\n+ --evalue $filter_score.bitscore\n+ #end if\n+\n+ --id $identity\n+ $sensitive\n+ --gapopen $method.gapopen\n+ --gapextend $method.gapextend\n+ --matrix $matrix\n+ $seg\n+ $salltitles\n+\n+]]>\n+ </command>\n+ <inputs>\n+\n+ <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />\n+\n+ <conditional name="ref_db_source">\n+ <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">\n+ <options from_data_table="diamond_database">\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+ </when> <!-- build-in -->\n+ <when value="history">\n+ <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" />\n+ </when> <!-- history -->\n+ </conditional>\n+\n+ <conditional name="method">\n+ <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">\n+ <option value="blastp">Align amino acid query sequences (blastp)</option>\n+ <option value="blastx">Align DNA query sequences (blastx)</option>\n+ </param>\n+ <when value="blastp">\n+ <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />\n+ <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />\n+ </when>\n+ <when value="blastx">\n+ <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />\n+ <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />\n+ </when>\n+ </conditional>\n+\n+ <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)">\n+ <option value="BLOSUM45">BLOSUM45</option>\n+ <option value="BLOSUM50">BLOSUM50</option>\n+ <option value="BLOSUM62" selected="True">BLOSUM62</option>\n+ <option value="BLOSUM80">BLOSUM80</option>\n+ <option value="BLOSUM90">BLOSUM90</option>\n+ <option value="PAM250">PAM250</option>\n+ <option value="PAM70'..b'<conditional name="filter_score">\n+ <param name="filter_score_select" type="select" label="Filter by score" help="(--evalue/--min-score)">\n+ <option value="evalue">Maximum e-value to report alignments</option>\n+ <option value="bit">Minimum bit score to report alignments</option>\n+ </param>\n+ <when value="evalue">\n+ <param name="evalue" type="float" value="0.001" label="Filter by evalue" help="(--evalue)" />\n+ </when>\n+ <when value="bit">\n+ <param name="bitscore" type="integer" value="0" label="Filter by bit score" help="(--min-score)" />\n+ </when>\n+ </conditional>\n+\n+ <conditional name="hit_filter">\n+ <param name="hit_filter_select" type="select" label="Restrict number of hits by" help="(--max-target-seqs/--top)">\n+ <option value="max">Maximum number of target sequences</option>\n+ <option value="percentage">Percentage of top alignment score</option>\n+ </param>\n+ <when value="max">\n+ <param name="max" type="integer" value="25" label="How many hits?" help="(--max-target-seqs)" />\n+ </when>\n+ <when value="percentage">\n+ <param name="percentage" type="integer" value="0" label="How many percentage" help="(--top)" />\n+ </when>\n+ </conditional>\n+\n+ <param name="identity" type="integer" value="0" label="minimum identity to report an alignment" help="in percentage (--id)" />\n+ <param name="salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="false"\n+ label="Print subject titles into the blast tabular format" help="(--salltitles)"/>\n+ <param name="seg" type="boolean" truevalue="--seg yes" falsevalue="--seg no" checked="true"\n+ label="Enable SEG masking of queries" help="(--seg)"/>\n+ <param name="sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false"\n+ label="Enable sensitive mode" help="(--sensitive)"/>\n+ </inputs>\n+ <outputs>\n+ <!--data format="sam" name="sam_output"/-->\n+ <data format="tabular" name="blast_output"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="method" value="blastp"/>\n+ <param name="query" value="protein.fasta" ftype="fasta"/>\n+ <param name="reference_database" value="diamond_makedb_result1.dmnd" ftype="diamond_database"/>\n+ <param name="db_source" value="history"/>\n+ <output name="blast_output" file="diamond_result1.tabular" ftpye="tabular"/>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.\n+On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting\n+about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500\n+times faster than BLASTX, finding more than 94% of all matches.\n+\n+.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/\n+\n+\n+Supported values for gap open and gap extend parameters depending on the selected scoring matrix.\n+\n+======== ============================================\n+Matrix Supported values for (gap open)/(gap extend)\n+======== ============================================\n+BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1\n+BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1\n+BLOSUM62 (6-11)/2; (9-13)/1\n+BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1\n+BLOSUM90 (6-9)/2; (9-11)/1\n+PAM250 (11-15)/3; (13-17)/2; (17-21)/1\n+PAM70 (6-8)/2; (9-11)/1\n+PAM30 (5-7)/2; (8-10)/1\n+======== ============================================\n+\n+\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/nmeth.3176</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 98037ef3d2a9 diamond_makedb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/diamond_makedb.xml Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,50 @@ +<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13"> + <description>Build database from a FASTA file</description> + <requirements> + <requirement type="package" version="0.6.13">diamond</requirement> + </requirements> + <command> + <!-- DB has two files, *.dmnd and *.tx --> +<![CDATA[ + diamond makedb + --threads "\${GALAXY_SLOTS:-12}" + --in $infile + --db ./database + && + mv ./database.dmnd $outfile +]]> + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" /> + </inputs> + + <outputs> + <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/> + </outputs> + <tests> + <test> + <param name="infile" value="protein.fasta" ftype="fasta"/> + <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/> + </test> + </tests> + <help> +<![CDATA[ + +.. class:: infomark + +**What it does** + +DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. +On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting +about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 +times faster than BLASTX, finding more than 94% of all matches. + +.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ + + +]]> + </help> + <citations> + <citation type="doi">10.1038/nmeth.3176</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 98037ef3d2a9 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the Diamond data manager."> + <repository changeset_revision="ce62d0912b10" name="data_manager_diamond_database_builder" owner="bgruening" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r 98037ef3d2a9 tool-data/diamond_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/diamond_database.loc.sample Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,10 @@ +#This is a sample file that enables the diamind to find the protein databases +#You will need to create these data files and then create +#a diamond_database.loc file similar to this one (store it in this directory) +#that points to the directories in which those files are stored. +#The diamond_database_indices.loc file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <display_name> <file_base_path> +# +#So, for example: +#ncbi_nr NCBI NR database (1-1-2015) /data/db/diamond/1-1-2015/nr.dmnd |
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| diff -r 000000000000 -r 98037ef3d2a9 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="diamond_database" comment_char="#"> + <columns>value, name, db_path</columns> + <file path="tool-data/diamond_database.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 98037ef3d2a9 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="diamond" version="0.6.13"> + <repository changeset_revision="47c4dfd5aed5" name="package_diamond_0_6_13" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |