| Previous changeset 14:8b8a3f793f0f (2025-08-04) Next changeset 16:1faba1aa14c1 (2025-12-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond commit 6f1673eb6a2735d23126919a313cc043e1107b2b |
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modified:
diamond.xml diamond_makedb.xml diamond_view.xml macros.xml |
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added:
test-data/db.fasta.gz test-data/protein.fasta.gz |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 diamond.xml --- a/diamond.xml Mon Aug 04 13:27:25 2025 +0000 +++ b/diamond.xml Mon Nov 10 15:12:53 2025 +0000 |
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| b'@@ -1,5 +1,5 @@\n-<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0">\n- <description>alignment tool for short sequences against a protein database</description>\n+<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1" license="GPL-3.0">\n+ <description>align short sequences against a protein database</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -13,9 +13,9 @@\n <![CDATA[\n \n #if $ref_db_source.db_source == "history":\n- ln -s $ref_db_source.reference_database ./database.dmnd\n+ ln -s \'$ref_db_source.reference_database\' ./database.dmnd\n #else:\n- ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd\n+ ln -s \'${ref_db_source.index.fields.db_path}\' ./database.dmnd\n #end if\n \n &&\n@@ -144,7 +144,7 @@\n <option value="31">Blastocrithidia Nuclear Code</option>\n <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option>\n </param>\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+ <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"/>\n <param name="query_strand" argument="--strand" type="select" label="query strands to search" help="">\n <option value="both" selected="True">Both</option>\n <option value="plus">Plus</option>\n@@ -177,7 +177,7 @@\n </param>\n </when>\n </conditional>\n- <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format"/>\n+ <param argument="--query" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" 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 database from your history or use a built-in index?" help="Built-ins were indexed using default options">\n <option value="indexed">Use a built-in index</option>\n@@ -336,8 +336,9 @@\n <test expect_num_outputs="3">\n <conditional name="method_cond">\n <param name="method_select" value="blastp"/>\n+ <param name="comp_based_stats" value="1"/>\n </conditional>\n- <param name="query" value="protein.fasta" ftype="fasta"/>\n+ <param name="query" value="protein.fasta.gz" ftype="fasta.gz"/>\n <conditional name="ref_db_source">\n <param name="db_source" value="history"/>\n <param name="reference_database" value="db-wtax.dmnd"/>\n@@ -346,14 +347,13 @@\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,scovhsp,sskingdoms,skingdoms,sphylums,cigar"/>\n- <param name="unal" value="true"/>\n </conditional>\n+ <param name="output_unal" value="--al,--un"/>\n </section>\n <conditional name="sens_cond">\n <param name="sensitivity" value=""/>\n </conditional>\n <param name="matrix" value="'..b' name="comp_based_stats" value="1"/>\n </conditional>\n <param name="query" value="protein.fasta" ftype="fasta"/>\n <conditional name="ref_db_source">\n@@ -405,7 +405,6 @@\n <param name="sensitivity" value=""/>\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="max"/>\n@@ -426,6 +425,7 @@\n <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastx"/>\n+ <param name="comp_based_stats" value="1"/>\n <conditional name="frameshift_cond">\n <param name="frameshift_select" value="yes"/>\n </conditional>\n@@ -444,7 +444,6 @@\n <param name="sensitivity" value=""/>\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@@ -474,8 +473,6 @@\n <section name="output_section">\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 </section>\n <output name="daa_output" file="diamond_results.daa" compare="sim_size" delta="10"/>\n@@ -484,6 +481,7 @@\n <test expect_num_outputs="1">\n <conditional name="method_cond">\n <param name="method_select" value="blastx"/>\n+ <param name="comp_based_stats" value="1"/>\n <conditional name="frameshift_cond">\n <param name="frameshift_select" value="yes"/>\n </conditional>\n@@ -502,7 +500,6 @@\n <param name="sensitivity" value=""/>\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@@ -605,8 +602,8 @@\n <param name="db_source" value="indexed"/>\n <param name="index" value="testDb"/>\n </conditional>\n- <param name="max_hsps" value="10"/>\n <section name="output_section">\n+ <param name="max_hsps" value="10"/>\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@@ -624,7 +621,9 @@\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="advanced_section">\n+ <param name="seed_cut" value="100"/>\n+ </section>\n <section name="output_section">\n <conditional name="output">\n <param name="outfmt" value="6"/>\n@@ -643,7 +642,9 @@\n <param name="db_source" value="indexed"/>\n <param name="index" value="testDb"/>\n </conditional>\n- <param name="freq_masking" value="true"/>\n+ <section name="advanced_section">\n+ <param name="freq_masking" value="true"/>\n+ </section>\n <section name="output_section">\n <conditional name="output">\n <param name="outfmt" value="6"/>\n' |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 diamond_makedb.xml --- a/diamond_makedb.xml Mon Aug 04 13:27:25 2025 +0000 +++ b/diamond_makedb.xml Mon Nov 10 15:12:53 2025 +0000 |
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| @@ -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"> |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 diamond_view.xml --- a/diamond_view.xml Mon Aug 04 13:27:25 2025 +0000 +++ b/diamond_view.xml Mon Nov 10 15:12:53 2025 +0000 |
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| @@ -67,9 +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> |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 macros.xml --- a/macros.xml Mon Aug 04 13:27:25 2025 +0000 +++ b/macros.xml Mon Nov 10 15:12:53 2025 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.1.13</token> - <token name="@VERSION_SUFFIX@">0</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> |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 test-data/db.fasta.gz |
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| Binary file test-data/db.fasta.gz has changed |
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| diff -r 8b8a3f793f0f -r 0cdcf7e99b62 test-data/protein.fasta.gz |
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| Binary file test-data/protein.fasta.gz has changed |