| Previous changeset 0:98037ef3d2a9 (2015-02-08) Next changeset 2:fd14bf35c9fd (2017-02-06) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e |
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modified:
diamond.xml diamond_makedb.xml repository_dependencies.xml |
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added:
macros.xml test-data/db.dmnd test-data/db.fasta test-data/diamond_results.tabular test-data/protein.fasta |
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removed:
tool_dependencies.xml |
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| diff -r 98037ef3d2a9 -r df7738595640 diamond.xml --- a/diamond.xml Sun Feb 08 10:05:26 2015 -0500 +++ b/diamond.xml Mon Feb 06 07:08:25 2017 -0500 |
| [ |
| b'@@ -1,8 +1,11 @@\n-<tool id="bg_diamond" name="Diamond" version="0.1.6.0">\n+<tool id="bg_diamond" name="Diamond" version="@VERSION@">\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+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" />\n <command>\n <![CDATA[\n \n@@ -15,41 +18,57 @@\n &&\n \n diamond\n- $method.method_select\n+ $method_select\n --threads "\\${GALAXY_SLOTS:-12}"\n --db ./database\n- --query $query\n- --out $blast_output\n- ##--sam $sam_output\n- --compress 0\n- --tmpdir ./\n+ --query \'$query\'\n+ --query-gencode \'$query_gencode\'\n+\n+ #if $output.outfmt == "5"\n+ --outfmt \'5\'\n+ --out \'$blast_xml\'\n+ $output.salltitles\n+ #else if $output.outfmt == "6"\n+ --outfmt \'6\' #echo \' \'.join(str($output.fields).split(\',\'))\n+ --out \'$blast_tabular\'\n+ #else if $output.outfmt == "101"\n+ --outfmt \'101\'\n+ --out \'$sam_output\'\n+ $output.salltitles\n+ #end if\n+\n+ --compress \'0\'\n+ $sensitive\n+ $more_sensitive\n+ --gapopen \'$gapopen\'\n+ --gapextend \'$gapextend\'\n+ --matrix \'$matrix\'\n+ --seg \'$seg\'\n \n #if str($hit_filter.hit_filter_select) == \'max\':\n- --max-target-seqs $hit_filter.max\n+ --max-target-seqs \'$hit_filter.max_target_seqs\'\n #else:\n- --top $hit_filter.percentage\n+ --top \'$hit_filter.top\'\n #end if\n \n #if str($filter_score.filter_score_select) == \'evalue\':\n- --evalue $filter_score.evalue\n+ --evalue \'$filter_score.evalue\'\n #else:\n- --evalue $filter_score.bitscore\n+ --min-score \'$filter_score.min_score\'\n #end if\n \n- --id $identity\n- $sensitive\n- --gapopen $method.gapopen\n- --gapextend $method.gapextend\n- --matrix $matrix\n- $seg\n- $salltitles\n-\n+ --id \'$id\'\n+ --query-cover \'$query_cover\'\n+ --block-size \'$block_size\'\n ]]>\n </command>\n+\n <inputs>\n-\n- <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />\n-\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+ <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />\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@@ -62,90 +81,160 @@\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>\n <when value="history">\n- <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" />\n- </when> <!-- history -->\n+ <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />\n+ </when>\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="bl'..b' 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+ <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">\n+ <filter>output["outfmt"] == "5"</filter>\n+ </data>\n+ <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">\n+ <filter>output["outfmt"] == "6"</filter>\n+ </data>\n+ <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">\n+ <filter>output["outfmt"] == "101"</filter>\n+ </data>\n </outputs>\n+\n <tests>\n <test>\n- <param name="method" value="blastp"/>\n+ <param name="method_select" 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+ <param name="reference_database" value="db.dmnd"/>\n+ <param name="query_gencode" value="1"/>\n+ <param name="outfmt" value="6"/>\n+ <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>\n+ <param name="sensitive" value=""/>\n+ <param name="more_sensitive" value=""/>\n+ <param name="gapopen" value="11"/>\n+ <param name="gapextend" value="1"/>\n+ <param name="matrix" value="BLOSUM62"/>\n+ <param name="seg" value="yes"/>\n+ <param name="hit_filter_select" value="max"/>\n+ <param name="max_target_seqs" value="25" />\n+ <param name="filter_score_select" value="evalue"/>\n+ <param name="evalue" value="0.001" />\n+ <param name="id" value="0"/>\n+ <param name="query_cover" value="0"/>\n+ <param name="block_size" value="2"/>\n+ <output name="blast_tabular" file="diamond_results.tabular"/>\n </test>\n </tests>\n+\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@@ -153,8 +242,33 @@\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+The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommend for small datasets.\n+\n .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/\n \n+**Input**\n+\n+Input data is a large protein or nucleotide sequence file.\n+\n+\n+**Output**\n+\n+Diamond gives you a tabular output file with 12 columns:\n+\n+Column \tDescription\n+1 \t Query Seq-id (ID of your sequence)\n+2 \t Subject Seq-id (ID of the database hit)\n+3 \t Percentage of identical matches\n+4 \t Alignment length\n+5 \t Number of mismatches\n+6 \t Number of gap openings\n+7 \t Start of alignment in query\n+8 \t End of alignment in query\n+9 \t Start of alignment in subject (database hit)\n+10 \t End of alignment in subject (database hit)\n+11 \t Expectation value (E-value)\n+12 \t Bit score\n+\n \n Supported values for gap open and gap extend parameters depending on the selected scoring matrix.\n \n@@ -174,7 +288,5 @@\n \n ]]>\n </help>\n- <citations>\n- <citation type="doi">10.1038/nmeth.3176</citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 98037ef3d2a9 -r df7738595640 diamond_makedb.xml --- a/diamond_makedb.xml Sun Feb 08 10:05:26 2015 -0500 +++ b/diamond_makedb.xml Mon Feb 06 07:08:25 2017 -0500 |
| [ |
| @@ -1,32 +1,38 @@ -<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13"> +<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@"> <description>Build database from a FASTA file</description> - <requirements> - <requirement type="package" version="0.6.13">diamond</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> <!-- DB has two files, *.dmnd and *.tx --> <![CDATA[ - diamond makedb + diamond makedb --threads "\${GALAXY_SLOTS:-12}" - --in $infile + --in '$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 ${on_string}"/> + <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/> </outputs> + <tests> <test> - <param name="infile" value="protein.fasta" ftype="fasta"/> - <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/> + <param name="infile" value="db.fasta" ftype="fasta"/> + <output name="outfile" value="db.dmnd"/> </test> </tests> + <help> <![CDATA[ @@ -36,7 +42,7 @@ 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 +about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500 times faster than BLASTX, finding more than 94% of all matches. .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ @@ -44,7 +50,6 @@ ]]> </help> - <citations> - <citation type="doi">10.1038/nmeth.3176</citation> - </citations> + + <expand macro="citations" /> </tool> |
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| diff -r 98037ef3d2a9 -r df7738595640 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 06 07:08:25 2017 -0500 |
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| @@ -0,0 +1,24 @@ +<macros> + <token name="@VERSION@">0.8.24</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">diamond</requirement> + </requirements> + </xml> + + <xml name="stdio"> + <stdio> + </stdio> + </xml> + + <xml name="version_command"> + <version_command>diamond version</version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.3176</citation> + </citations> + </xml> +</macros> |
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| diff -r 98037ef3d2a9 -r df7738595640 repository_dependencies.xml --- a/repository_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 +++ b/repository_dependencies.xml Mon Feb 06 07:08:25 2017 -0500 |
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| @@ -1,4 +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" /> + <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 98037ef3d2a9 -r df7738595640 test-data/db.dmnd |
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| Binary file test-data/db.dmnd has changed |
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| diff -r 98037ef3d2a9 -r df7738595640 test-data/db.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/db.fasta Mon Feb 06 07:08:25 2017 -0500 |
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| @@ -0,0 +1,6 @@ +>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY |
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| diff -r 98037ef3d2a9 -r df7738595640 test-data/diamond_results.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.tabular Mon Feb 06 07:08:25 2017 -0500 |
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| @@ -0,0 +1,1 @@ +sequence gi|5524211|gb|AAD44166.1| 90.5 284 26 1 1 283 1 284 1.0e-152 521.2 |
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| diff -r 98037ef3d2a9 -r df7738595640 test-data/protein.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein.fasta Mon Feb 06 07:08:25 2017 -0500 |
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| @@ -0,0 +1,6 @@ +>sequence +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY |
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| diff -r 98037ef3d2a9 -r df7738595640 tool_dependencies.xml --- a/tool_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?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> |