Mercurial > repos > p.lucas > diamond_using_binary

changeset 40:ae2a362dd513 draft

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Uploaded
author p.lucas
date Tue, 04 Jun 2024 12:58:51 +0000
parents 47de63bff362
children b5a8cc7a993f
files diamond.xml
diffstat 1 files changed, 332 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/diamond.xml	Tue Jun 04 12:57:37 2024 +0000
+++ b/diamond.xml	Tue Jun 04 12:58:51 2024 +0000
@@ -1,8 +1,12 @@
-<tool id="pl_diamond" name="PL_Diamond" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
+<tool id="bg_diamond" name="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">
@@ -16,7 +20,7 @@
 
     &&
 
-    /usr/bin/diamond
+    diamond
         $method_cond.method_select
         --quiet
         --threads "\${GALAXY_SLOTS:-12}"
@@ -174,7 +178,7 @@
             </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="pl_diamond_database">
+                    <options from_data_table="diamond_database">
                         <filter type="sort_by" column="2"/>
                         <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                     </options>
@@ -314,6 +318,331 @@
             <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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