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diff busco.xml @ 19:1b5840963240 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a
author iuc
date Fri, 30 Aug 2024 15:19:29 +0000
parents 0e63a4c4c908
children 9da899448a8a
line wrap: on
line diff
--- a/busco.xml	Fri Apr 14 08:13:19 2023 +0000
+++ b/busco.xml	Fri Aug 30 15:19:29 2024 +0000
@@ -14,7 +14,7 @@
     <version_command>busco --version</version_command>
     <command><![CDATA[
 
-#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
+#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus':
 
 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
@@ -35,12 +35,11 @@
 --cpu \${GALAXY_SLOTS:-4}
 --evalue ${adv.evalue}
 --limit ${adv.limit}
+--contig_break ${adv.contig_break}
 
 #if $lineage_conditional.selector == 'cached':
     --offline
     --download_path $lineage_conditional.cached_db.fields.path
-#else
-    --update-data
 #end if
 
 #if $lineage.lineage_mode == "auto_detect":
@@ -48,18 +47,24 @@
 #else if $lineage.lineage_mode == "select_lineage":
     --lineage_dataset '${lineage.lineage_dataset}'
 #end if
-#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
 
-    ${busco_mode.use_augustus.long}
-    --augustus
+#if $busco_mode.mode == 'geno':
+    #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot':
+        --miniprot
+    #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
+        ${busco_mode.use_augustus.long}
+        --augustus
 
-    #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
-        --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
-    #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
-        --augustus_species local
+        #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
+            --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
+        #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
+            --augustus_species local
+        #end if
+    #else:
+        --metaeuk
     #end if
 #end if
-
+    
 #if $outputs and 'image' in $outputs:
     &&
     mkdir BUSCO_summaries
@@ -78,6 +83,7 @@
     cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
 #end if
 
+
 ]]>    </command>
     <inputs>
         <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
@@ -103,12 +109,15 @@
             </param>
             <when value="geno">
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
-                        <option value="yes">Yes, use Augustus</option>
-                        <option value="no" selected="true">Use Metaeuk</option>
+                    <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">
+                        <option value="augustus">Augustus</option>
+                        <option value="metaeuk">Metaeuk</option>
+                        <option value="miniprot" selected="true">Miniprot</option>
+
                     </param>
-                    <when value="no" />
-                    <when value="yes">
+                    <when value="metaeuk"/>
+                    <when value="miniprot"/>
+                    <when value="augustus">
                         <conditional name="aug_prediction">
                             <param name="augustus_mode" type="select" label="Augustus species model">
                                 <option value="no" selected="true">Use the default species for selected lineage</option>
@@ -162,8 +171,10 @@
         <section name="adv" title="Advanced Options" expanded="False">
             <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
             <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
+            <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
         </section>
     </inputs>
+
     <outputs>
         <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
             <filter>outputs and 'short_summary' in outputs</filter>
@@ -177,8 +188,9 @@
         </data>
         <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
             <filter>outputs and 'gff' in outputs</filter>
-        </data>
+        </data>              
     </outputs>
+    
     <tests>
         <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
@@ -189,23 +201,24 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="Gene predictor used: augustus"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
                     <has_text text="##gff-version 3" />
                 </assert_contents>
             </output>
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
-                <assert_contents>
-                    <has_text text="# BUSCO version is: @TOOL_VERSION@" />
-                </assert_contents>
-            </output>
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="proteome.fa" />
@@ -217,9 +230,14 @@
                 <param name="mode" value="prot" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="BUSCO was run in mode: proteins" />
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" />
             <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
             <output name="busco_gff">
                 <assert_contents>
@@ -238,7 +256,11 @@
                 <param name="mode" value="tran" />
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="BUSCO was run in mode: euk_tran" />
+                </assert_contents>
+            </output>
             <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
             <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
@@ -253,7 +275,7 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                     <conditional name="aug_prediction">
                         <param name="augustus_mode" value="builtin" />
                         <param name="augustus_species" value="human" />
@@ -261,8 +283,12 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,gff" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: augustus"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
@@ -279,7 +305,7 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="yes" />
+                    <param name="use_augustus_selector" value="augustus" />
                     <conditional name="aug_prediction">
                         <param name="augustus_mode" value="history" />
                         <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
@@ -287,9 +313,14 @@
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing" />
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: augustus"/>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" />
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
@@ -300,15 +331,29 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="no" />
+                    <param name="use_augustus_selector" value="metaeuk" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
-            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
-            <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
-            <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: metaeuk"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table" file="genome_results_metaeuk/full_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
+            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
+            <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
+            <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />
         </test>
         <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
@@ -319,32 +364,49 @@
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="no" />
+                    <param name="use_augustus_selector" value="metaeuk" />
                 </conditional>
             </conditional>
             <param name="outputs" value="short_summary,missing,image,gff" />
-            <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
-            <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="Gene predictor used: metaeuk"/>
+                </assert_contents>
+            </output>
+            <output name="busco_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="The lineage dataset is: eukaryota_odb10"/>
+                </assert_contents>
+            </output>
+            <output name="busco_missing">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="The lineage dataset is: eukaryota_odb10"/>
+                </assert_contents>
+            </output>
             <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
             <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
-            <conditional name="lineage_conditional">
-                <param name="selector" value="cached"/>
-                <param name="cached_db" value="busco-demo-db-20230328"/>
-            </conditional>
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="archaea_odb10" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
             </conditional>
-            <param name="outputs" value="short_summary" />
-            <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />
-            <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />
-            <assert_stdout>
-                <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>
-            </assert_stdout>
+            <param name="outputs" value="short_summary,gff" />
+            <output name="busco_sum">
+                <assert_contents>
+                    <has_text text="# Gene predictor used: miniprot"/>
+                </assert_contents>
+            </output>
+            <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />
+            <output name="busco_table" file="genome_results_miniprot/full_table">
+                <assert_contents>
+                    <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+                    <has_text text="9647at6656"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[