Mercurial > repos > bgruening > diamond
changeset 1:df7738595640 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
| author | bgruening |
|---|---|
| date | Mon, 06 Feb 2017 07:08:25 -0500 |
| parents | 98037ef3d2a9 |
| children | fd14bf35c9fd |
| files | diamond.xml diamond_makedb.xml macros.xml repository_dependencies.xml test-data/db.dmnd test-data/db.fasta test-data/diamond_results.tabular test-data/protein.fasta tool_dependencies.xml |
| diffstat | 9 files changed, 256 insertions(+), 108 deletions(-) [+] |
line wrap: on
line diff
--- a/diamond.xml Sun Feb 08 10:05:26 2015 -0500 +++ b/diamond.xml Mon Feb 06 07:08:25 2017 -0500 @@ -1,8 +1,11 @@ -<tool id="bg_diamond" name="Diamond" version="0.1.6.0"> +<tool id="bg_diamond" name="Diamond" version="@VERSION@"> <description>alignment tool for short sequences against a protein database</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> <![CDATA[ @@ -15,41 +18,57 @@ && diamond - $method.method_select + $method_select --threads "\${GALAXY_SLOTS:-12}" --db ./database - --query $query - --out $blast_output - ##--sam $sam_output - --compress 0 - --tmpdir ./ + --query '$query' + --query-gencode '$query_gencode' + + #if $output.outfmt == "5" + --outfmt '5' + --out '$blast_xml' + $output.salltitles + #else if $output.outfmt == "6" + --outfmt '6' #echo ' '.join(str($output.fields).split(',')) + --out '$blast_tabular' + #else if $output.outfmt == "101" + --outfmt '101' + --out '$sam_output' + $output.salltitles + #end if + + --compress '0' + $sensitive + $more_sensitive + --gapopen '$gapopen' + --gapextend '$gapextend' + --matrix '$matrix' + --seg '$seg' #if str($hit_filter.hit_filter_select) == 'max': - --max-target-seqs $hit_filter.max + --max-target-seqs '$hit_filter.max_target_seqs' #else: - --top $hit_filter.percentage + --top '$hit_filter.top' #end if #if str($filter_score.filter_score_select) == 'evalue': - --evalue $filter_score.evalue + --evalue '$filter_score.evalue' #else: - --evalue $filter_score.bitscore + --min-score '$filter_score.min_score' #end if - --id $identity - $sensitive - --gapopen $method.gapopen - --gapextend $method.gapextend - --matrix $matrix - $seg - $salltitles - + --id '$id' + --query-cover '$query_cover' + --block-size '$block_size' ]]> </command> + <inputs> - - <param name="query" type="data" format="fasta" label="Input query file in FASTA format" /> - + <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)"> + <option value="blastp">Align amino acid query sequences (blastp)</option> + <option value="blastx">Align DNA query sequences (blastx)</option> + </param> + <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> <conditional name="ref_db_source"> <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"> <option value="indexed">Use a built-in index</option> @@ -62,90 +81,160 @@ <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> - </when> <!-- build-in --> + </when> <when value="history"> - <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" /> - </when> <!-- history --> + <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> + </when> </conditional> - - <conditional name="method"> - <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> - <option value="blastp">Align amino acid query sequences (blastp)</option> - <option value="blastx">Align DNA query sequences (blastx)</option> + <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help=""> + <option value="1">The Standard Code</option> + <option value="2">The Vertebrate Mitochondrial Code</option> + <option value="3">The Yeast Mitochondrial Code</option> + <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">The Invertebrate Mitochondrial Code</option> + <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option> + <option value="10">The Euplotid Nuclear Code</option> + <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option> + <option value="12">The Alternative Yeast Nuclear Code</option> + <option value="13">The Ascidian Mitochondrial Code</option> + <option value="14">The Alternative Flatworm Mitochondrial Code</option> + <option value="16">Chlorophycean Mitochondrial Code</option> + <option value="21">Trematode Mitochondrial Code</option> + <option value="22">Scenedesmus obliquus Mitochondrial Code</option> + <option value="23">Thraustochytrium Mitochondrial Code</option> + <option value="24">Pterobranchia Mitochondrial Code</option> + <option value="5">Candidate Division SR1 and Gracilibacteria Code</option> + <option value="26">Pachysolen tannophilus Nuclear Code</option> + </param> + <conditional name="output"> + <param argument="--outfmt" type="select" label="Format of output file " help=""> + <option value="5">BLAST XML</option> + <option value="6">BLAST tabular</option> + <option value="101">SAM</option> </param> - <when value="blastp"> - <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> - <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> + <when value="5"> + <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> </when> - <when value="blastx"> - <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> - <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> + <when value="6"> + <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> + <option value="qseqid" selected="true">Query Seq - id</option> + <option value="sseqid" selected="true">Subject Seq - id</option> + <option value="sallseqid">All subject Seq - id(s)</option> + <option value="qlen">Query sequence length</option> + <option value="slen">Subject sequence length</option> + <option value="pident" selected="true">Percentage of identical matches</option> + <option value="length" selected="true">Alignment length</option> + <option value="nident">Number of identical matches</option> + <option value="mismatch" selected="true">Number of mismatches</option> + <option value="positive">Number of positive - scoring matches</option> + <option value="gapopen" selected="true">Number of gap openings</option> + <option value="gaps">Total number of gaps</option> + <option value="ppos">Percentage of positive - scoring matches</option> + <option value="qstart" selected="true">Start of alignment in query</option> + <option value="qend" selected="true">End of alignment in query</option> + <option value="sstart" selected="true">Start of alignment in subject</option> + <option value="send" selected="true">End of alignment in subject</option> + <option value="qseq">Aligned part of query sequence</option> + <option value="sseq">Aligned part of subject sequence</option> + <option value="evalue" selected="true">Expect value</option> + <option value="bitscore" selected="true">Bit score</option> + <option value="score">Raw score</option> + <option value="qframe">Query frame</option> + <option value="stitle">Subject Title</option> + <option value="salltitles">All Subject Title(s)</option> + <option value="qcovhsp">Query Coverage Per HSP</option> + </param> + </when> + <when value="101"> + <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> </when> </conditional> - - <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)"> - <option value="BLOSUM45">BLOSUM45</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM62" selected="True">BLOSUM62</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM90">BLOSUM90</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> + <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/> + <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/> + <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" /> + <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" /> + <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)"> + <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option> + <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option> + <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option> + <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option> + <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option> + <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option> + <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option> + <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option> </param> - + <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/> + <conditional name="hit_filter"> + <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> + <option value="max">Maximum number of target sequences</option> + <option value="top">Percentage of top alignment score</option> + </param> + <when value="max"> + <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to keep alignments for" help="" /> + </when> + <when value="top"> + <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" /> + </when> + </conditional> <conditional name="filter_score"> - <param name="filter_score_select" type="select" label="Filter by score" help="(--evalue/--min-score)"> + <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> <option value="evalue">Maximum e-value to report alignments</option> - <option value="bit">Minimum bit score to report alignments</option> + <option value="min-score">Minimum bit score to report alignments</option> </param> <when value="evalue"> - <param name="evalue" type="float" value="0.001" label="Filter by evalue" help="(--evalue)" /> - </when> - <when value="bit"> - <param name="bitscore" type="integer" value="0" label="Filter by bit score" help="(--min-score)" /> + <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" /> </when> - </conditional> - - <conditional name="hit_filter"> - <param name="hit_filter_select" type="select" label="Restrict number of hits by" help="(--max-target-seqs/--top)"> - <option value="max">Maximum number of target sequences</option> - <option value="percentage">Percentage of top alignment score</option> - </param> - <when value="max"> - <param name="max" type="integer" value="25" label="How many hits?" help="(--max-target-seqs)" /> - </when> - <when value="percentage"> - <param name="percentage" type="integer" value="0" label="How many percentage" help="(--top)" /> + <when value="min-score"> + <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" /> </when> </conditional> + <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" /> + <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" /> + <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" /> + </inputs> - <param name="identity" type="integer" value="0" label="minimum identity to report an alignment" help="in percentage (--id)" /> - <param name="salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="false" - label="Print subject titles into the blast tabular format" help="(--salltitles)"/> - <param name="seg" type="boolean" truevalue="--seg yes" falsevalue="--seg no" checked="true" - label="Enable SEG masking of queries" help="(--seg)"/> - <param name="sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" - label="Enable sensitive mode" help="(--sensitive)"/> - </inputs> <outputs> - <!--data format="sam" name="sam_output"/--> - <data format="tabular" name="blast_output"/> + <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> + <filter>output["outfmt"] == "5"</filter> + </data> + <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> + <filter>output["outfmt"] == "6"</filter> + </data> + <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> + <filter>output["outfmt"] == "101"</filter> + </data> </outputs> + <tests> <test> - <param name="method" value="blastp"/> + <param name="method_select" value="blastp" /> <param name="query" value="protein.fasta" ftype="fasta"/> - <param name="reference_database" value="diamond_makedb_result1.dmnd" ftype="diamond_database"/> <param name="db_source" value="history"/> - <output name="blast_output" file="diamond_result1.tabular" ftpye="tabular"/> + <param name="reference_database" value="db.dmnd"/> + <param name="query_gencode" value="1"/> + <param name="outfmt" value="6"/> + <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> + <param name="sensitive" value=""/> + <param name="more_sensitive" value=""/> + <param name="gapopen" value="11"/> + <param name="gapextend" value="1"/> + <param name="matrix" value="BLOSUM62"/> + <param name="seg" value="yes"/> + <param name="hit_filter_select" value="max"/> + <param name="max_target_seqs" value="25" /> + <param name="filter_score_select" value="evalue"/> + <param name="evalue" value="0.001" /> + <param name="id" value="0"/> + <param name="query_cover" value="0"/> + <param name="block_size" value="2"/> + <output name="blast_tabular" file="diamond_results.tabular"/> </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. @@ -153,8 +242,33 @@ 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. +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. + .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ +**Input** + +Input data is a large protein or nucleotide sequence file. + + +**Output** + +Diamond gives you a tabular output file with 12 columns: + +Column Description +1 Query Seq-id (ID of your sequence) +2 Subject Seq-id (ID of the database hit) +3 Percentage of identical matches +4 Alignment length +5 Number of mismatches +6 Number of gap openings +7 Start of alignment in query +8 End of alignment in query +9 Start of alignment in subject (database hit) +10 End of alignment in subject (database hit) +11 Expectation value (E-value) +12 Bit score + Supported values for gap open and gap extend parameters depending on the selected scoring matrix. @@ -174,7 +288,5 @@ ]]> </help> - <citations> - <citation type="doi">10.1038/nmeth.3176</citation> - </citations> + <expand macro="citations" /> </tool>
--- 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 06 07:08:25 2017 -0500 @@ -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>
--- a/repository_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 +++ b/repository_dependencies.xml Mon Feb 06 07:08:25 2017 -0500 @@ -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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/db.fasta Mon Feb 06 07:08:25 2017 -0500 @@ -0,0 +1,6 @@ +>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results.tabular Mon Feb 06 07:08:25 2017 -0500 @@ -0,0 +1,1 @@ +sequence gi|5524211|gb|AAD44166.1| 90.5 284 26 1 1 283 1 284 1.0e-152 521.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein.fasta Mon Feb 06 07:08:25 2017 -0500 @@ -0,0 +1,6 @@ +>sequence +LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV +EWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG +LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL +GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX +IENY
--- a/tool_dependencies.xml Sun Feb 08 10:05:26 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>