| Previous changeset 8:54f751e413f4 (2021-03-22) Next changeset 10:1e3323a44643 (2022-04-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3" |
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modified:
diamond.xml diamond_makedb.xml diamond_view.xml macros.xml test-data/diamond_results.tabular test-data/protein.fasta |
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| diff -r 54f751e413f4 -r f921014aba5a diamond.xml --- a/diamond.xml Mon Mar 22 13:21:23 2021 +0000 +++ b/diamond.xml Sat Nov 27 09:48:10 2021 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="bg_diamond" name="Diamond" version="@VERSION@.0" profile="19.01">\n+<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@.1" profile="19.01">\n <description>alignment tool for short sequences against a protein database</description>\n <macros>\n <import>macros.xml</import>\n@@ -62,8 +62,23 @@\n --query-cover \'$query_cover\'\n --subject-cover \'$subject_cover\'\n --block-size \'$sens_cond.block_size\'\n- #if str($unal) == \'1\':\n- --unal 1 --un \'$unalqueries\'\n+ #if $output_unal\n+ #if "--un" in $output_unal\n+ --un \'$unalqueries\'\n+ #if $query.ext.startswith("fasta"):\n+ --unfmt fasta\n+ #else\n+ --unfmt fastq\n+ #end if\n+ #end if\n+ #if "--al" in $output_unal\n+ --al \'$alqueries\'\n+ #if $query.ext.startswith("fasta"):\n+ --alfmt fasta\n+ #else\n+ --alfmt fastq\n+ #end if\n+ #end if\n #end if\n #if $tax_cond.tax_select == \'file\':\n --taxonlist `cat \'$tax_cond.taxonlistfile\' | grep -v "^#" | grep -v "^$" | tr "\\n" "," | sed \'s/,$//\'`\n@@ -79,7 +94,7 @@\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+ <param 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@@ -100,7 +115,7 @@\n <option value="25">Candidate Division SR1 and Gracilibacteria Code</option>\n <option value="26">Pachysolen tannophilus Nuclear Code</option>\n </param>\n- <param argument="--min-orf" name="min_orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />\n+ <param argument="--min-orf" type="integer" value="1" label="ignore translated sequences without an open reading frame of at least this length" help="By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1 will disable this feature" />\n \n <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">\n <option value="both" selected="True">Both</option>\n@@ -113,21 +128,21 @@\n <option value="no" selected="true">no</option>\n </param>\n <when value="yes">\n- <param argument="--range-culling" name="range_culling" type="boolean" truevalue="--range-culling" falsevalue="" checked="false" label="restrict hit culling to overlapping query ranges" help="This feature is designed for long query DNA sequences that may span several genes. In these cases, the default of reporting the 25 best overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing the number of alignments reported will bloat the output size and reduce performance. Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its query range is spanned by at least 25 higher or equal scoring hits. Using this featur'..b' <param name="unal" value="true"/>\n </conditional>\n <conditional name="sens_cond">\n <param name="sensitivity" value=""/>\n </conditional>\n <param name="matrix" value="BLOSUM62"/>\n- <param name="comp-based-stat" value="1"/>\n+ <param name="comp_based_stats" value="1"/>\n <param name="masking" value="1"/>\n <conditional name="hit_filter">\n <param name="hit_filter_select" value="max"/>\n@@ -277,9 +300,20 @@\n <conditional name="sens_cond">\n <param name="block_size" value="2"/>\n </conditional>\n+ <param name="output_unal" value="--al,--un"/>\n+ <output name="unalqueries">\n+ <assert_contents>\n+ <has_line line=">shuffled sequence that should go to unaligned"/>\n+ </assert_contents>\n+ </output>\n+ <output name="alqueries">\n+ <assert_contents>\n+ <has_line line=">sequence more text"/>\n+ </assert_contents>\n+ </output>\n <output name="blast_tabular" file="diamond_results.tabular"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastp" />\n </conditional>\n@@ -300,7 +334,7 @@\n <param name="sensitivity" value=""/>\n </conditional>\n <param name="matrix" value="BLOSUM62"/>\n- <param name="comp-based-stat" value="1"/>\n+ <param name="comp_based_stats" value="1"/>\n <param name="masking" value="1"/>\n <conditional name="hit_filter">\n <param name="hit_filter_select" value="max"/>\n@@ -317,7 +351,7 @@\n </conditional>\n <output name="blast_tabular" file="diamond_results.wtax.tabular"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastx" />\n <conditional name="frameshift_cond">\n@@ -336,7 +370,7 @@\n <param name="sensitivity" value=""/>\n </conditional>\n <param name="matrix" value="BLOSUM62"/>\n- <param name="comp-based-stat" value="1"/>\n+ <param name="comp_based_stats" value="1"/>\n <param name="masking" value="1"/>\n <conditional name="hit_filter">\n <param name="hit_filter_select" value="top"/>\n@@ -353,7 +387,7 @@\n </conditional>\n <output name="blast_tabular" file="diamond_results.pairwise"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastp" />\n </conditional>\n@@ -364,10 +398,12 @@\n </conditional>\n <conditional name="output">\n <param name="outfmt" value="100"/>\n+ <param name="salltitles" value="false"/>\n+ <param name="sallseqid" value="false"/>\n </conditional>\n <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>\n </test>\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastx" />\n <conditional name="frameshift_cond">\n@@ -386,7 +422,7 @@\n <param name="sensitivity" value=""/>\n </conditional>\n <param name="matrix" value="BLOSUM62"/>\n- <param name="comp-based-stat" value="1"/>\n+ <param name="comp_based_stats" value="1"/>\n <param name="masking" value="1"/>\n <conditional name="hit_filter">\n <param name="hit_filter_select" value="top"/>\n' |
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| diff -r 54f751e413f4 -r f921014aba5a diamond_makedb.xml --- a/diamond_makedb.xml Mon Mar 22 13:21:23 2021 +0000 +++ b/diamond_makedb.xml Sat Nov 27 09:48:10 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@" profile="19.01"> +<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@" profile="19.01"> <description>Build database from a FASTA file</description> <macros> <import>macros.xml</import> |
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| diff -r 54f751e413f4 -r f921014aba5a diamond_view.xml --- a/diamond_view.xml Mon Mar 22 13:21:23 2021 +0000 +++ b/diamond_view.xml Sat Nov 27 09:48:10 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_view" name="Diamond view" version="@VERSION@" profile="19.01"> +<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@.1" profile="19.01"> <description>generate formatted output from DAA files</description> <macros> <import>macros.xml</import> @@ -29,7 +29,7 @@ <expand macro="output_macro" /> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> <conditional name="output"> <param name="outfmt" value="5"/> @@ -40,7 +40,7 @@ </conditional> <output name="blast_tabular" file="diamond_results.xml"/> </test> - <test> + <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> <conditional name="output"> <param name="outfmt" value="6"/> @@ -48,7 +48,7 @@ </conditional> <output name="blast_tabular" file="diamond_view_results.tabular"/> </test> - <test> + <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> <conditional name="output"> <param name="outfmt" value="101"/> |
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| diff -r 54f751e413f4 -r f921014aba5a macros.xml --- a/macros.xml Mon Mar 22 13:21:23 2021 +0000 +++ b/macros.xml Sat Nov 27 09:48:10 2021 +0000 |
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| @@ -1,9 +1,9 @@ <macros> - <token name="@VERSION@">2.0.8</token> + <token name="@TOOL_VERSION@">2.0.8</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">diamond</requirement> + <requirement type="package" version="@TOOL_VERSION@">diamond</requirement> </requirements> </xml> @@ -69,6 +69,7 @@ <option value="cigar">Cigar</option> <yield/> </param> + <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/> </when> <when value="100"> <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> @@ -99,11 +100,11 @@ </xml> <xml name="block_size_low_sens"> - <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="" /> + <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" /> </xml> <xml name="block_size_hi_sens"> - <param name="block_size" argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" /> + <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" /> </xml> <xml name="citations"> @@ -145,11 +146,16 @@ #else if $output.outfmt == "6" --outfmt '6' #echo ' '.join(str($output.fields).split(',')) --out '$blast_tabular' + --unal $output.unal #else if $output.outfmt == "100" --outfmt '100' + $output.salltitles + $output.sallseqid --out output.daa #else if $output.outfmt == "101" --outfmt '101' + $output.salltitles + $output.sallseqid --out '$sam_output' #else if $output.outfmt == "102" --outfmt '102' |
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| diff -r 54f751e413f4 -r f921014aba5a test-data/diamond_results.tabular --- a/test-data/diamond_results.tabular Mon Mar 22 13:21:23 2021 +0000 +++ b/test-data/diamond_results.tabular Sat Nov 27 09:48:10 2021 +0000 |
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| @@ -1,2 +1,3 @@ -sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 94M1D189M 100 0 0 0 -sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 105M1D178M 100 0 0 0 +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 100 0 0 0 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 100 0 0 0 +shuffled * -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 * * * |
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| diff -r 54f751e413f4 -r f921014aba5a test-data/protein.fasta --- a/test-data/protein.fasta Mon Mar 22 13:21:23 2021 +0000 +++ b/test-data/protein.fasta Sat Nov 27 09:48:10 2021 +0000 |
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| @@ -4,3 +4,9 @@ LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY +>shuffled sequence that should go to unaligned +XLPLILMLLGISPGSFEHTVAGGIWTSLMLFLPGYPGVGFLMLLVITVPALNFKFGFMLL +LKPTTNIIKTLVLALTHADDPLSFPWLNYMPPAADFNGLFTNAGATTTLYQIPYEGSFYL +AAIYGSMLHENHYLYRSMTPVGWLHLGDSGLRFMLLPIYYARITYDNVPAGWFLSVNTIL +GLTAILLEAIKALMANYSESQEPFCFSTGMKHSFIISDILGWDMSLYIILLIPHTNPFVL +TFLTLILWLDILSRYTLLQVNLIIFMTRHGHFQIADIWYWLKS |