# HG changeset patch
# User iuc
# Date 1762787552 0
# Node ID 7058b4f32f501aa6356f9d291e33c7c4fd0dac4c
# Parent  3f75f7bc764d71cdefdaeb600e9c18dd87d2241e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond commit 6f1673eb6a2735d23126919a313cc043e1107b2b

diff -r 3f75f7bc764d -r 7058b4f32f50 diamond.xml
--- 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="&gt;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"/>
diff -r 3f75f7bc764d -r 7058b4f32f50 diamond_makedb.xml
--- 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">
diff -r 3f75f7bc764d -r 7058b4f32f50 diamond_view.xml
--- 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="&lt;BlastOutput_version&gt;diamond @TOOL_VERSION@&lt;/BlastOutput_version&gt;"/>
+                </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>
diff -r 3f75f7bc764d -r 7058b4f32f50 macros.xml
--- 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>
diff -r 3f75f7bc764d -r 7058b4f32f50 test-data/db.fasta.gz
Binary file test-data/db.fasta.gz has changed
diff -r 3f75f7bc764d -r 7058b4f32f50 test-data/diamond_results.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), &quot;Fast and sensitive protein alignment using DIAMOND&quot;, 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
diff -r 3f75f7bc764d -r 7058b4f32f50 test-data/protein.fasta.gz
Binary file test-data/protein.fasta.gz has changed