| Previous changeset 9:f921014aba5a (2021-11-27) Next changeset 11:e8ac2b53f262 (2023-11-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01" |
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modified:
diamond.xml diamond_makedb.xml diamond_view.xml macros.xml test-data/db-wtax.dmnd test-data/db.dmnd test-data/diamond_results.daa test-data/diamond_results.sam test-data/diamond_results.xml test-data/diamond_view_results.tabular |
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added:
test-data/diamond_results_algorithm.tabular test-data/diamond_results_freq_masking.tabular test-data/diamond_results_global_ranking.tabular test-data/diamond_results_iterate.tabular test-data/diamond_results_max_hsps.tabular test-data/diamond_results_motif_masking.tabular test-data/diamond_results_seed_cut.tabular |
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| diff -r f921014aba5a -r 1e3323a44643 diamond.xml --- a/diamond.xml Sat Nov 27 09:48:10 2021 +0000 +++ b/diamond.xml Fri Apr 22 13:51:34 2022 +0000 |
| b |
| b'@@ -1,4 +1,4 @@\n-<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@.1" profile="19.01">\n+<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">\n <description>alignment tool for short sequences against a protein database</description>\n <macros>\n <import>macros.xml</import>\n@@ -37,9 +37,15 @@\n \n @OUTPUT_ARGS@\n \n- --compress \'0\'\n+ #if $output_section.output.outfmt != \'100\'\n+ --compress \'0\'\n+ #end if\n $sens_cond.sensitivity\n-\n+ $iterate\n+ --algo $algo\n+ #if $global_ranking\n+ --global-ranking $global_ranking\n+ #end if\n #if str($gapopen) != "":\n --gapopen \'$gapopen\'\n #end if\n@@ -62,8 +68,8 @@\n --query-cover \'$query_cover\'\n --subject-cover \'$subject_cover\'\n --block-size \'$sens_cond.block_size\'\n- #if $output_unal\n- #if "--un" in $output_unal\n+ #if $output_section.output_unal\n+ #if "--un" in $output_section.output_unal\n --un \'$unalqueries\'\n #if $query.ext.startswith("fasta"):\n --unfmt fasta\n@@ -71,7 +77,7 @@\n --unfmt fastq\n #end if\n #end if\n- #if "--al" in $output_unal\n+ #if "--al" in $output_section.output_unal\n --al \'$alqueries\'\n #if $query.ext.startswith("fasta"):\n --alfmt fasta\n@@ -80,33 +86,41 @@\n #end if\n #end if\n #end if\n+ #if $output_section.max_hsps\n+ --max-hsps $output_section.max_hsps\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 #else if $tax_cond.tax_select == \'list\':\n --taxonlist \'$tax_cond.taxonlist\'\n #end if\n+ #if $advanced_section.seed_cut\n+ --seed-cut $advanced_section.seed_cut\n+ #end if\n+ $advanced_section.freq_masking\n+ --motif-masking $advanced_section.motif_masking\n ]]>\n </command>\n <inputs>\n <conditional name="method_cond">\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 name="method_select" type="select" label="Alignment mode" help="(blastp/blastx)">\n+ <option value="blastp">Amino acid query sequences (blastp)</option>\n+ <option value="blastx">DNA query sequences (blastx)</option>\n </param>\n <when value="blastx">\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- <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- '..b' </section>\n+ <output name="blast_tabular" file="diamond_results_max_hsps.tabular"/>\n+ </test>\n+ <!--Test 10 seed-cut option-->\n+ <test expect_num_outputs="1">\n+ <conditional name="method_cond">\n+ <param name="method_select" value="blastx" />\n </conditional>\n- <conditional name="sens_cond">\n- <param name="sensitivity" value=""/>\n+ <param name="query" value="nucleotide.fasta" ftype="fasta"/>\n+ <conditional name="ref_db_source">\n+ <param name="db_source" value="indexed"/>\n+ <param name="index" value="testDb"/>\n+ </conditional>\n+ <param name="seed_cut" value="100"/>\n+ <section name="output_section">\n+ <conditional name="output">\n+ <param name="outfmt" value="6"/>\n+ <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>\n+ </conditional>\n+ </section>\n+ <output name="blast_tabular" file="diamond_results_seed_cut.tabular"/>\n+ </test>\n+ <!--Test 11 freq-masking option-->\n+ <test expect_num_outputs="1">\n+ <conditional name="method_cond">\n+ <param name="method_select" value="blastx" />\n </conditional>\n- <param name="matrix" value="BLOSUM62"/>\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- <param name="top" value="10" />\n+ <param name="query" value="nucleotide.fasta" ftype="fasta"/>\n+ <conditional name="ref_db_source">\n+ <param name="db_source" value="indexed"/>\n+ <param name="index" value="testDb"/>\n </conditional>\n- <conditional name="filter_score">\n- <param name="filter_score_select" value="min-score"/>\n- <param name="min_score" value="1" />\n+ <param name="freq_masking" value="true"/>\n+ <section name="output_section">\n+ <conditional name="output">\n+ <param name="outfmt" value="6"/>\n+ <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>\n+ </conditional>\n+ </section>\n+ <output name="blast_tabular" file="diamond_results_freq_masking.tabular"/>\n+ </test>\n+ <!--Test 12 motif-masking option-->\n+ <test expect_num_outputs="1">\n+ <conditional name="method_cond">\n+ <param name="method_select" value="blastx" />\n </conditional>\n- <param name="id" value="0"/>\n- <param name="query_cover" value="0"/>\n- <conditional name="sens_cond">\n- <param name="block_size" value="2"/>\n+ <param name="query" value="nucleotide.fasta" ftype="fasta"/>\n+ <conditional name="ref_db_source">\n+ <param name="db_source" value="indexed"/>\n+ <param name="index" value="testDb"/>\n </conditional>\n- <output name="blast_tabular" file="diamond_results.pairwise"/>\n+ <section name="advanced_section">\n+ <param name="motif_masking" value="1"/>\n+ </section>\n+ <section name="output_section">\n+ <conditional name="output">\n+ <param name="outfmt" value="6"/>\n+ <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>\n+ </conditional>\n+ </section>\n+ <output name="blast_tabular" file="diamond_results_motif_masking.tabular"/>\n </test>\n </tests>\n <help>\n' |
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| diff -r f921014aba5a -r 1e3323a44643 diamond_makedb.xml --- a/diamond_makedb.xml Sat Nov 27 09:48:10 2021 +0000 +++ b/diamond_makedb.xml Fri Apr 22 13:51:34 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@" profile="19.01"> +<tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01"> <description>Build database from a FASTA file</description> <macros> <import>macros.xml</import> @@ -32,9 +32,12 @@ <option value="no" selected="true">No</option> </param> <when value="yes"> - <param argument="--taxonmap" type="data" format="tabular" label="protein accession to taxid mapping file" help="" /> - <param argument="--taxonnodes" type="data" format="tabular" label="taxonomy nodes.dmp from NCBI" help="" /> - <param argument="--taxonnames" type="data" format="tabular" label="taxonomy names.dmp from NCBI" help="" /> + <param argument="--taxonmap" type="data" format="tabular" + label="Protein accession to taxid mapping file" + help="Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. + A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored" /> + <param argument="--taxonnodes" type="data" format="tabular" label="Taxonomy nodes.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" /> + <param argument="--taxonnames" type="data" format="tabular" label="Taxonomy names.dmp from NCBI" help="This parameter is optional and needs to be supplied in order to provide taxonomy features" /> </when> <when value="no"/> </conditional> @@ -76,7 +79,7 @@ .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ -- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz +- taxonmap: Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz - taxonnames: Path to the names.dmp file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip |
| b |
| diff -r f921014aba5a -r 1e3323a44643 diamond_view.xml --- a/diamond_view.xml Sat Nov 27 09:48:10 2021 +0000 +++ b/diamond_view.xml Fri Apr 22 13:51:34 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@.1" profile="19.01"> +<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01"> <description>generate formatted output from DAA files</description> <macros> <import>macros.xml</import> @@ -21,7 +21,9 @@ </command> <inputs> <param argument="--daa" type="data" format="daa" label="input file in DAA format" /> - <expand macro="output_type_macro" /> + <section name="output_section" title="Output options"> + <expand macro="output_type_macro" /> + </section> <expand macro="hit_filter_macro" /> <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/> </inputs> @@ -31,9 +33,11 @@ <tests> <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> - <conditional name="output"> - <param name="outfmt" value="5"/> - </conditional> + <section name="output_section"> + <conditional name="output"> + <param name="outfmt" value="5"/> + </conditional> + </section> <conditional name="hit_filter"> <param name="hit_filter_select" value="max"/> <param name="max_target_seqs" value="1" /> @@ -42,17 +46,21 @@ </test> <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> - <conditional name="output"> - <param name="outfmt" value="6"/> - <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/> - </conditional> + <section name="output_section"> + <conditional name="output"> + <param name="outfmt" value="6"/> + <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/> + </conditional> + </section> <output name="blast_tabular" file="diamond_view_results.tabular"/> </test> <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa" /> - <conditional name="output"> - <param name="outfmt" value="101"/> - </conditional> + <section name="output_section"> + <conditional name="output"> + <param name="outfmt" value="101"/> + </conditional> + </section> <conditional name="hit_filter"> <param name="hit_filter_select" value="top"/> <param name="max_target_seqs" value="1" /> |
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| diff -r f921014aba5a -r 1e3323a44643 macros.xml --- a/macros.xml Sat Nov 27 09:48:10 2021 +0000 +++ b/macros.xml Fri Apr 22 13:51:34 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.0.8</token> - + <token name="@TOOL_VERSION@">2.0.15</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">diamond</requirement> @@ -19,7 +19,7 @@ <xml name="output_type_macro"> <conditional name="output"> - <param argument="--outfmt" type="select" label="Format of output file " help=""> + <param argument="--outfmt" type="select" label="Format of output file" help=""> <option value="0">BLAST pairwise</option> <option value="5">BLAST XML</option> <option value="6">BLAST tabular</option> @@ -90,21 +90,26 @@ <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 report alignments for" help="Setting this to 0 will report all alignments that were found." /> + <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" + help="Setting this to 0 will report all alignments that were found." /> </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 query" help="For example, setting this to 10 will report all align- -ments whose score is at most 10% lower than the best alignment score for a query." /> + <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" + help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query." /> </when> </conditional> </xml> <xml name="block_size_low_sens"> - <param 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="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary + disk space, but also improve performance" /> </xml> <xml name="block_size_hi_sens"> - <param 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="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary + disk space, but also improve performance" /> </xml> <xml name="citations"> @@ -116,48 +121,48 @@ <xml name="output_macro"> <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> - <filter>output["outfmt"] == "0"</filter> + <filter>output_section["output"]["outfmt"] == "0"</filter> </data> <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> - <filter>output["outfmt"] == "5"</filter> + <filter>output_section["output"]["outfmt"] == "5"</filter> </data> <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> - <filter>output["outfmt"] == "6"</filter> + <filter>output_section["output"]["outfmt"] == "6"</filter> </data> <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> - <filter>output["outfmt"] == "100"</filter> + <filter>output_section["output"]["outfmt"] == "100"</filter> </data> <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> - <filter>output["outfmt"] == "101"</filter> + <filter>output_section["output"]["outfmt"] == "101"</filter> </data> <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> - <filter>output["outfmt"] == "102"</filter> + <filter>output_section["output"]["outfmt"] == "102"</filter> </data> </xml> <token name="@OUTPUT_ARGS@"> - #if $output.outfmt == "0" + #if $output_section.output.outfmt == "0" --outfmt '0' --out '$blast_pairw' - #else if $output.outfmt == "5" + #else if $output_section.output.outfmt == "5" --outfmt '5' --out '$blast_xml' - #else if $output.outfmt == "6" - --outfmt '6' #echo ' '.join(str($output.fields).split(',')) + #else if $output_section.output.outfmt == "6" + --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(',')) --out '$blast_tabular' - --unal $output.unal - #else if $output.outfmt == "100" + --unal $output_section.output.unal + #else if $output_section.output.outfmt == "100" --outfmt '100' - $output.salltitles - $output.sallseqid + $output_section.output.salltitles + $output_section.output.sallseqid --out output.daa - #else if $output.outfmt == "101" + #else if $output_section.output.outfmt == "101" --outfmt '101' - $output.salltitles - $output.sallseqid + $output_section.output.salltitles + $output_section.output.sallseqid --out '$sam_output' - #else if $output.outfmt == "102" + #else if $output_section.output.outfmt == "102" --outfmt '102' --out '$tax_output' #end if |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/db-wtax.dmnd |
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| Binary file test-data/db-wtax.dmnd has changed |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/db.dmnd |
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| Binary file test-data/db.dmnd has changed |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results.daa |
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| Binary file test-data/diamond_results.daa has changed |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results.sam --- a/test-data/diamond_results.sam Sat Nov 27 09:48:10 2021 +0000 +++ b/test-data/diamond_results.sam Fri Apr 22 13:51:34 2022 +0000 |
| b |
| @@ -1,5 +1,5 @@ @HD VN:1.5 SO:query -@PG PN:DIAMOND VN:2.0.8 CL:diamond view --threads 1 --daa input.daa --outfmt 101 --out /tmp/tmpz1aqzru3/files/3/f/6/dataset_3f6f43ac-3af2-4ec2-93be-9ced0e692b43.dat --top 0 --forwardonly --compress 0 +@PG PN:DIAMOND VN:2.0.15 CL:diamond view --threads 1 --daa input.daa --outfmt 101 --salltitles --sallseqid --out /tmp/tmpuqw24dac/files/e/4/b/dataset_e4b47568-a2e4-4ec1-ac5f-f266085686a4.dat --top 0 --forwardonly --compress 0 @mm BlastP @CO BlastP-like alignments @CO Reporting AS: bitScore, ZR: rawScore, ZE: expected, ZI: percent identity, ZL: reference length, ZF: frame, ZS: query start DNA coordinate |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results.xml --- a/test-data/diamond_results.xml Sat Nov 27 09:48:10 2021 +0000 +++ b/test-data/diamond_results.xml Fri Apr 22 13:51:34 2022 +0000 |
| b |
| @@ -2,7 +2,7 @@ <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput> <BlastOutput_program>blastp</BlastOutput_program> - <BlastOutput_version>diamond 2.0.8</BlastOutput_version> + <BlastOutput_version>diamond 2.0.15</BlastOutput_version> <BlastOutput_reference>Benjamin Buchfink, Xie Chao, and Daniel Huson (2015), "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12:59-60.</BlastOutput_reference> <BlastOutput_db></BlastOutput_db> <BlastOutput_query-ID>Query_1</BlastOutput_query-ID> @@ -28,7 +28,7 @@ <Hit_num>1</Hit_num> <Hit_id>gi|5524211|gb|AAD44166.1|</Hit_id> <Hit_def></Hit_def> - <Hit_accession>AAD44166.1</Hit_accession> + <Hit_accession>AAD44166</Hit_accession> <Hit_len>284</Hit_len> <Hit_hsps> <Hsp> |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_algorithm.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_algorithm.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_freq_masking.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_freq_masking.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_global_ranking.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_global_ranking.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_iterate.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_iterate.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_max_hsps.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_max_hsps.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_results_motif_masking.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diamond_results_motif_masking.tabular Fri Apr 22 13:51:34 2022 +0000 |
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| @@ -0,0 +1,2 @@ +sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 849 1 284 1.44e-205 550 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 849 1 284 5.77e-150 409 |
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| diff -r f921014aba5a -r 1e3323a44643 test-data/diamond_view_results.tabular --- a/test-data/diamond_view_results.tabular Sat Nov 27 09:48:10 2021 +0000 +++ b/test-data/diamond_view_results.tabular Fri Apr 22 13:51:34 2022 +0000 |
| b |
| @@ -1,2 +1,2 @@ sequence gi|5524211|gb|AAD44166.1| 99.6 284 0 1 1 283 1 284 1.44e-205 550 94M1D189M 100 -sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 83M1D200M 100 +sequence gi|5524212|gb|AAD44167.1| 79.6 284 57 1 1 283 1 284 5.77e-150 409 105M1D178M 100 |