Mercurial > repos > bgruening > diamond
changeset 22:7058b4f32f50 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond commit 6f1673eb6a2735d23126919a313cc043e1107b2b
| author | iuc |
|---|---|
| date | Mon, 10 Nov 2025 15:12:32 +0000 |
| parents | 3f75f7bc764d |
| children | |
| files | diamond.xml diamond_makedb.xml diamond_view.xml macros.xml test-data/db.fasta.gz test-data/diamond_results.xml test-data/protein.fasta.gz |
| diffstat | 7 files changed, 36 insertions(+), 95 deletions(-) [+] |
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--- a/diamond.xml Tue Jun 10 13:51:43 2025 +0000 +++ b/diamond.xml Mon Nov 10 15:12:32 2025 +0000 @@ -1,5 +1,5 @@ -<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0"> - <description>alignment tool for short sequences against a protein database</description> +<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1" license="GPL-3.0"> + <description>align short sequences against a protein database</description> <macros> <import>macros.xml</import> </macros> @@ -13,9 +13,9 @@ <![CDATA[ #if $ref_db_source.db_source == "history": - ln -s $ref_db_source.reference_database ./database.dmnd + ln -s '$ref_db_source.reference_database' ./database.dmnd #else: - ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd + ln -s '${ref_db_source.index.fields.db_path}' ./database.dmnd #end if && @@ -144,7 +144,7 @@ <option value="31">Blastocrithidia Nuclear Code</option> <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option> </param> - <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"/> + <param argument="--min-orf" type="integer" value="1" min="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"/> <param name="query_strand" argument="--strand" type="select" label="query strands to search" help=""> <option value="both" selected="True">Both</option> <option value="plus">Plus</option> @@ -177,7 +177,7 @@ </param> </when> </conditional> - <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format"/> + <param argument="--query" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" 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 database 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> @@ -336,8 +336,9 @@ <test expect_num_outputs="3"> <conditional name="method_cond"> <param name="method_select" value="blastp"/> + <param name="comp_based_stats" value="1"/> </conditional> - <param name="query" value="protein.fasta" ftype="fasta"/> + <param name="query" value="protein.fasta.gz" ftype="fasta.gz"/> <conditional name="ref_db_source"> <param name="db_source" value="history"/> <param name="reference_database" value="db-wtax.dmnd"/> @@ -346,14 +347,13 @@ <conditional name="output"> <param name="outfmt" value="6"/> <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,scovhsp,sskingdoms,skingdoms,sphylums,cigar"/> - <param name="unal" value="true"/> </conditional> + <param name="output_unal" value="--al,--un"/> </section> <conditional name="sens_cond"> <param name="sensitivity" value=""/> </conditional> <param name="matrix" value="BLOSUM62"/> - <param name="comp_based_stats" value="1"/> <param name="masking" value="1"/> <conditional name="hit_filter"> <param name="hit_filter_select" value="max"/> @@ -368,7 +368,6 @@ <conditional name="sens_cond"> <param name="block_size" value="2"/> </conditional> - <param name="output_unal" value="--al,--un"/> <output name="unalqueries"> <assert_contents> <has_line line=">shuffled sequence that should go to unaligned"/> @@ -385,6 +384,7 @@ <test expect_num_outputs="1"> <conditional name="method_cond"> <param name="method_select" value="blastp"/> + <param name="comp_based_stats" value="1"/> </conditional> <param name="query" value="protein.fasta" ftype="fasta"/> <conditional name="ref_db_source"> @@ -405,7 +405,6 @@ <param name="sensitivity" value=""/> </conditional> <param name="matrix" value="BLOSUM62"/> - <param name="comp_based_stats" value="1"/> <param name="masking" value="1"/> <conditional name="hit_filter"> <param name="hit_filter_select" value="max"/> @@ -426,6 +425,7 @@ <test expect_num_outputs="1"> <conditional name="method_cond"> <param name="method_select" value="blastx"/> + <param name="comp_based_stats" value="1"/> <conditional name="frameshift_cond"> <param name="frameshift_select" value="yes"/> </conditional> @@ -444,7 +444,6 @@ <param name="sensitivity" value=""/> </conditional> <param name="matrix" value="BLOSUM62"/> - <param name="comp_based_stats" value="1"/> <param name="masking" value="1"/> <conditional name="hit_filter"> <param name="hit_filter_select" value="top"/> @@ -474,8 +473,6 @@ <section name="output_section"> <conditional name="output"> <param name="outfmt" value="100"/> - <param name="salltitles" value="false"/> - <param name="sallseqid" value="false"/> </conditional> </section> <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/> @@ -484,6 +481,7 @@ <test expect_num_outputs="1"> <conditional name="method_cond"> <param name="method_select" value="blastx"/> + <param name="comp_based_stats" value="1"/> <conditional name="frameshift_cond"> <param name="frameshift_select" value="yes"/> </conditional> @@ -502,7 +500,6 @@ <param name="sensitivity" value=""/> </conditional> <param name="matrix" value="BLOSUM62"/> - <param name="comp_based_stats" value="1"/> <param name="masking" value="1"/> <conditional name="hit_filter"> <param name="hit_filter_select" value="top"/> @@ -605,8 +602,8 @@ <param name="db_source" value="indexed"/> <param name="index" value="testDb"/> </conditional> - <param name="max_hsps" value="10"/> <section name="output_section"> + <param name="max_hsps" value="10"/> <conditional name="output"> <param name="outfmt" value="6"/> <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> @@ -624,7 +621,9 @@ <param name="db_source" value="indexed"/> <param name="index" value="testDb"/> </conditional> - <param name="seed_cut" value="100"/> + <section name="advanced_section"> + <param name="seed_cut" value="100"/> + </section> <section name="output_section"> <conditional name="output"> <param name="outfmt" value="6"/> @@ -643,7 +642,9 @@ <param name="db_source" value="indexed"/> <param name="index" value="testDb"/> </conditional> - <param name="freq_masking" value="true"/> + <section name="advanced_section"> + <param name="freq_masking" value="true"/> + </section> <section name="output_section"> <conditional name="output"> <param name="outfmt" value="6"/>
--- a/diamond_makedb.xml Tue Jun 10 13:51:43 2025 +0000 +++ b/diamond_makedb.xml Mon Nov 10 15:12:32 2025 +0000 @@ -1,5 +1,5 @@ <tool id="bg_diamond_makedb" name="Diamond makedb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0"> - <description>Build database from a FASTA file</description> + <description>build database from a FASTA file</description> <macros> <import>macros.xml</import> </macros> @@ -22,7 +22,7 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format"/> + <param name="infile" type="data" format="fasta,fasta.gz" label="Input reference file in FASTA format"/> <conditional name="tax_cond"> <param name="tax_select" type="select" label="Add taxonomic data?" help="Needs to be supplied in order to provide taxonomy features of the aligner"> <option value="yes">Yes</option> @@ -44,6 +44,11 @@ <param name="infile" value="db.fasta" ftype="fasta"/> <output name="outfile" value="db.dmnd" compare="sim_size" delta="2"/> </test> + + <test> + <param name="infile" value="db.fasta.gz" ftype="fasta.gz"/> + <output name="outfile" value="db.dmnd" compare="sim_size" delta="2"/> + </test> <test> <param name="infile" value="db.fasta" ftype="fasta"/> <conditional name="tax_cond">
--- a/diamond_view.xml Tue Jun 10 13:51:43 2025 +0000 +++ b/diamond_view.xml Mon Nov 10 15:12:32 2025 +0000 @@ -42,7 +42,11 @@ <param name="hit_filter_select" value="max"/> <param name="max_target_seqs" value="1"/> </conditional> - <output name="blast_tabular" file="diamond_results.xml"/> + <output name="blast_tabular"> + <assert_contents> + <has_text text="<BlastOutput_version>diamond @TOOL_VERSION@</BlastOutput_version>"/> + </assert_contents> + </output> </test> <test expect_num_outputs="1"> <param name="daa" ftype="daa" value="diamond_results.daa"/> @@ -63,9 +67,9 @@ </section> <conditional name="hit_filter"> <param name="hit_filter_select" value="top"/> - <param name="max_target_seqs" value="1"/> + <param name="top" value="1"/> </conditional> - <param name="forwardonly" value="--forwardonly"/> + <param name="forwardonly" value="true"/> <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/> </test> </tests>
--- a/macros.xml Tue Jun 10 13:51:43 2025 +0000 +++ b/macros.xml Mon Nov 10 15:12:32 2025 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">2.1.12</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.1.13</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">diamond</requirement> @@ -88,7 +88,7 @@ <param 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 alignments whose score is at most 10% lower than the best alignment score for a query."/> + <param argument="--top" type="integer" value="0" min="0" max="100" 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>
--- a/test-data/diamond_results.xml Tue Jun 10 13:51:43 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -<?xml version="1.0"?> -<!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 2.1.12</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> - <BlastOutput_query-def>sequence</BlastOutput_query-def> - <BlastOutput_query-len>283</BlastOutput_query-len> - <BlastOutput_param> - <Parameters> - <Parameters_matrix>blosum62</Parameters_matrix> - <Parameters_expect>0.001</Parameters_expect> - <Parameters_gap-open>11</Parameters_gap-open> - <Parameters_gap-extend>1</Parameters_gap-extend> - <Parameters_filter>F</Parameters_filter> - </Parameters> - </BlastOutput_param> -<BlastOutput_iterations> -<Iteration> - <Iteration_iter-num>1</Iteration_iter-num> - <Iteration_query-ID>Query_1</Iteration_query-ID> - <Iteration_query-def>sequence</Iteration_query-def> - <Iteration_query-len>283</Iteration_query-len> -<Iteration_hits> -<Hit> - <Hit_num>1</Hit_num> - <Hit_id>gi|5524211|gb|AAD44166.1|</Hit_id> - <Hit_def></Hit_def> - <Hit_accession>AAD44166</Hit_accession> - <Hit_len>284</Hit_len> - <Hit_hsps> - <Hsp> - <Hsp_num>1</Hsp_num> - <Hsp_bit-score>550</Hsp_bit-score> - <Hsp_score>1417</Hsp_score> - <Hsp_evalue>1.44e-205</Hsp_evalue> - <Hsp_query-from>1</Hsp_query-from> - <Hsp_query-to>283</Hsp_query-to> - <Hsp_hit-from>1</Hsp_hit-from> - <Hsp_hit-to>284</Hsp_hit-to> - <Hsp_query-frame>0</Hsp_query-frame> - <Hsp_hit-frame>0</Hsp_hit-frame> - <Hsp_identity>283</Hsp_identity> - <Hsp_positive>283</Hsp_positive> - <Hsp_gaps>1</Hsp_gaps> - <Hsp_align-len>284</Hsp_align-len> - <Hsp_qseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL-FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_qseq> - <Hsp_hseq>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_hseq> - <Hsp_midline>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFIL FTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILXXXXXXXALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY</Hsp_midline> - </Hsp> - </Hit_hsps> -</Hit> -</Iteration_hits> - <Iteration_stat> - <Statistics> - <Statistics_db-num>2</Statistics_db-num> - <Statistics_db-len>568</Statistics_db-len> - <Statistics_hsp-len>0</Statistics_hsp-len> - <Statistics_eff-space>0</Statistics_eff-space> - <Statistics_kappa>0.041000</Statistics_kappa> - <Statistics_lambda>0.267000</Statistics_lambda> - <Statistics_entropy>0</Statistics_entropy> - </Statistics> - </Iteration_stat> -</Iteration> -</BlastOutput_iterations> -</BlastOutput> \ No newline at end of file