| Previous changeset 2:fd14bf35c9fd (2017-02-06) Next changeset 4:cc30b68c0495 (2017-07-26) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0 |
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modified:
diamond.xml |
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removed:
diamond.tar.gz test-data/diamond_makedb_result1.dmnd |
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| diff -r fd14bf35c9fd -r 830516f9521b diamond.tar.gz |
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| Binary file diamond.tar.gz has changed |
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| diff -r fd14bf35c9fd -r 830516f9521b diamond.xml --- a/diamond.xml Mon Feb 06 23:57:32 2017 -0500 +++ b/diamond.xml Wed Jul 26 10:30:52 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bg_diamond" name="Diamond" version="@VERSION@">\n+<tool id="bg_diamond" name="Diamond" version="@VERSION@.1">\n <description>alignment tool for short sequences against a protein database</description>\n <macros>\n <import>macros.xml</import>\n@@ -18,11 +18,13 @@\n &&\n \n diamond\n- $method_select\n+ $method_select.method_select\n --threads "\\${GALAXY_SLOTS:-12}"\n --db ./database\n --query \'$query\'\n- --query-gencode \'$query_gencode\'\n+ #if $method_select.method_select == "blastx"\n+ --query-gencode \'$query_gencode\'\n+ #end if\n \n #if $output.outfmt == "5"\n --outfmt \'5\'\n@@ -38,8 +40,12 @@\n #end if\n \n --compress \'0\'\n- $sensitive\n- $more_sensitive\n+ #if $sensitivity == "1"\n+ --sensitive\n+ #else if $sensitivity == "2"\n+ --more-sensitive\n+ #end if\n+\n --gapopen \'$gapopen\'\n --gapextend \'$gapextend\'\n --matrix \'$matrix\'\n@@ -64,18 +70,45 @@\n </command>\n \n <inputs>\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+ <conditional name="method_select">\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="blastx">\n+ <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">\n+ <option value="1">The Standard Code</option>\n+ <option value="2">The Vertebrate Mitochondrial Code</option>\n+ <option value="3">The Yeast Mitochondrial Code</option>\n+ <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>\n+ <option value="5">The Invertebrate Mitochondrial Code</option>\n+ <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>\n+ <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>\n+ <option value="10">The Euplotid Nuclear Code</option>\n+ <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>\n+ <option value="12">The Alternative Yeast Nuclear Code</option>\n+ <option value="13">The Ascidian Mitochondrial Code</option>\n+ <option value="14">The Alternative Flatworm Mitochondrial Code</option>\n+ <option value="16">Chlorophycean Mitochondrial Code</option>\n+ <option value="21">Trematode Mitochondrial Code</option>\n+ <option value="22">Scenedesmus obliquus Mitochondrial Code</option>\n+ <option value="23">Thraustochytrium Mitochondrial Code</option>\n+ <option value="24">Pterobranchia Mitochondrial Code</option>\n+ <option value="5">Candidate Division SR1 and Gracilibacteria Code</option>\n+ <option value="26">Pachysolen tannophilus Nuclear Code</option>\n+ </param>\n+ </when>\n+ <when value="blastp">\n+ </when>\n+ </conditional>\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+ '..b' Euplotid Nuclear Code</option>\n- <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>\n- <option value="12">The Alternative Yeast Nuclear Code</option>\n- <option value="13">The Ascidian Mitochondrial Code</option>\n- <option value="14">The Alternative Flatworm Mitochondrial Code</option>\n- <option value="16">Chlorophycean Mitochondrial Code</option>\n- <option value="21">Trematode Mitochondrial Code</option>\n- <option value="22">Scenedesmus obliquus Mitochondrial Code</option>\n- <option value="23">Thraustochytrium Mitochondrial Code</option>\n- <option value="24">Pterobranchia Mitochondrial Code</option>\n- <option value="5">Candidate Division SR1 and Gracilibacteria Code</option>\n- <option value="26">Pachysolen tannophilus Nuclear Code</option>\n- </param>\n <conditional name="output">\n <param argument="--outfmt" type="select" label="Format of output file " help="">\n <option value="5">BLAST XML</option>\n@@ -150,8 +162,11 @@\n <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>\n </when>\n </conditional>\n- <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/>\n- <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."/>\n+ <param name=\'sensitivity\' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. More sensitivity may increase computation time">\n+ <option value="0" selected="True">Default</option>\n+ <option value="1">Sensitive</option>\n+ <option value="2">More Sensitive</option>\n+ </param>\n <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />\n <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />\n <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">\n@@ -212,11 +227,9 @@\n <param name="query" value="protein.fasta" ftype="fasta"/>\n <param name="db_source" value="history"/>\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="sensitivity" value="0"/>\n <param name="gapopen" value="11"/>\n <param name="gapextend" value="1"/>\n <param name="matrix" value="BLOSUM62"/>\n@@ -242,7 +255,7 @@\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+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 recommended for small datasets.\n \n .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/\n \n' |
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| diff -r fd14bf35c9fd -r 830516f9521b test-data/diamond_makedb_result1.dmnd |
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| Binary file test-data/diamond_makedb_result1.dmnd has changed |