# HG changeset patch
# User p.lucas
# Date 1717505981 0
# Node ID b5a8cc7a993f6af966a9fb11df65132842e6b444
# Parent  ae2a362dd513699b676404d25885b62ea91e42aa
Uploaded

diff -r ae2a362dd513 -r b5a8cc7a993f diamond.xml
--- a/diamond.xml	Tue Jun 04 12:58:51 2024 +0000
+++ b/diamond.xml	Tue Jun 04 12:59:41 2024 +0000
@@ -1,12 +1,8 @@
-<tool id="bg_diamond" name="Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+<tool id="pl_diamond" name="PL_Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
     <description>alignment tool for short sequences against a protein database</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <xrefs>
-        <xref type="bio.tools">diamond</xref>
-    </xrefs>
-    <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command detect_errors="aggressive">
@@ -20,7 +16,7 @@
 
     &&
 
-    diamond
+    /usr/bin/diamond
         $method_cond.method_select
         --quiet
         --threads "\${GALAXY_SLOTS:-12}"
@@ -178,7 +174,7 @@
             </param>
             <when value="indexed">
                 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin">
-                    <options from_data_table="diamond_database">
+                    <options from_data_table="pl_diamond_database">
                         <filter type="sort_by" column="2"/>
                         <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                     </options>
@@ -318,331 +314,6 @@
             <filter>output_section['output_unal'] and "--un" in output_section['output_unal']</filter>
         </data>
     </outputs>
-    <tests>
-        <!--Test 01-->
-        <test expect_num_outputs="3">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastp" />
-            </conditional>
-            <param name="query" value="protein.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="history"/>
-                <param name="reference_database" value="db-wtax.dmnd"/>
-            </conditional>
-            <section name="output_section">
-                <conditional name="output">
-                    <param name="outfmt" value="6"/>
-                    <!-- removed ,cigar from test: https://github.com/bbuchfink/diamond/issues/532 -->
-                    <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,scovhsp,sskingdoms,skingdoms,sphylums"/>
-                    <param name="unal" value="true"/>
-                </conditional>
-            </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"/>
-                <param name="max_target_seqs" value="25" />
-            </conditional>
-            <conditional name="filter_score">
-                <param name="filter_score_select" value="evalue"/>
-                <param name="evalue" value="0.001" />
-            </conditional>
-            <param name="id" value="0"/>
-            <param name="query_cover" value="0"/>
-            <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"/>
-                </assert_contents>
-            </output>
-            <output name="alqueries">
-                <assert_contents>
-                    <has_line line=">sequence more text"/>
-                </assert_contents>
-            </output>
-            <output name="blast_tabular" file="diamond_results.tabular"/>
-        </test>
-        <!--Test 02-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastp" />
-            </conditional>
-            <param name="query" value="protein.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="history"/>
-                <param name="reference_database" value="db-wtax.dmnd"/>
-            </conditional>
-            <conditional name="tax_cond">
-                <param name="tax_select" value="list"/>
-                <param name="taxonlist" value="2" />
-            </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"/>
-                </conditional>
-            </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"/>
-                <param name="max_target_seqs" value="25" />
-            </conditional>
-            <conditional name="filter_score">
-                <param name="filter_score_select" value="evalue"/>
-                <param name="evalue" value="0.001" />
-            </conditional>
-            <param name="id" value="0"/>
-            <param name="query_cover" value="0"/>
-            <conditional name="sens_cond">
-                <param name="block_size" value="2"/>
-            </conditional>
-            <output name="blast_tabular" file="diamond_results.wtax.tabular"/>
-        </test>
-        <!--Test 03-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-                <conditional name="frameshift_cond">
-                    <param name="frameshift_select" value="yes"/>
-                </conditional>
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="history"/>
-                <param name="reference_database" value="db.dmnd"/>
-            </conditional>
-            <section name="output_section">
-                <conditional name="output">
-                    <param name="outfmt" value="0"/>
-                </conditional>
-            </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="top"/>
-                <param name="top" value="10" />
-            </conditional>
-            <conditional name="filter_score">
-                <param name="filter_score_select" value="min-score"/>
-                <param name="min_score" value="1" />
-            </conditional>
-            <param name="id" value="0"/>
-            <param name="query_cover" value="0"/>
-            <conditional name="sens_cond">
-                <param name="block_size" value="2"/>
-            </conditional>
-            <output name="blast_tabular" file="diamond_results.pairwise"/>
-        </test>
-        <!--Test 04-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastp" />
-            </conditional>
-            <param name="query" value="protein.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="history"/>
-                <param name="reference_database" value="db-wtax.dmnd"/>
-            </conditional>
-            <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"/>
-        </test>
-        <!--Test 05-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-                <conditional name="frameshift_cond">
-                    <param name="frameshift_select" value="yes"/>
-                </conditional>
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <section name="output_section">
-                <conditional name="output">
-                    <param name="outfmt" value="0"/>
-                </conditional>
-            </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="top"/>
-                <param name="top" value="10" />
-            </conditional>
-            <conditional name="filter_score">
-                <param name="filter_score_select" value="min-score"/>
-                <param name="min_score" value="1" />
-            </conditional>
-            <param name="id" value="0"/>
-            <param name="query_cover" value="0"/>
-            <conditional name="sens_cond">
-                <param name="block_size" value="2"/>
-            </conditional>
-            <output name="blast_tabular" file="diamond_results.pairwise"/>
-        </test>
-        <!-- Test 06 iterate option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="iterate" value="true"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_iterate.tabular"/>
-        </test>
-        <!--Test 07 algo option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="algo" value="1"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_algorithm.tabular"/>
-        </test>
-        <!--Test 08 global-ranking option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="global_ranking" value="10"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_global_ranking.tabular"/>
-        </test>
-        <!--Test 09 max-hsps option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="max_hsps" value="10"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_max_hsps.tabular"/>
-        </test>
-        <!--Test 10 seed-cut option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="seed_cut" value="100"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_seed_cut.tabular"/>
-        </test>
-        <!--Test 11 freq-masking option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <param name="freq_masking" value="true"/>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_freq_masking.tabular"/>
-        </test>
-        <!--Test 12 motif-masking option-->
-        <test expect_num_outputs="1">
-            <conditional name="method_cond">
-                <param name="method_select" value="blastx" />
-            </conditional>
-            <param name="query" value="nucleotide.fasta" ftype="fasta"/>
-            <conditional name="ref_db_source">
-                <param name="db_source" value="indexed"/>
-                <param name="index" value="testDb"/>
-            </conditional>
-            <section name="advanced_section">
-                <param name="motif_masking" value="1"/>
-            </section>
-            <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"/>
-                </conditional>
-            </section>
-            <output name="blast_tabular" file="diamond_results_motif_masking.tabular"/>
-        </test>
-    </tests>
     <help>
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