busco: busco.xml comparison

comparison busco.xml @ 22:5dd4f18b0d96 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5

author	iuc
date	Sat, 04 Oct 2025 17:47:40 +0000
parents	c209d02621e7
children

comparison

equal deleted inserted replaced

-:c209d02621e7
+:5dd4f18b0d96
 ## a more thorough test can be executed as follows
 ## - set the `test` parameters to `""`
 ## - download complete reference DB (~200G, final 105G) to tools/busco/test-data/test-db/busco_downloads
 ##   ```
 ##   busco --download_path tools/busco/test-data/test-db/busco_downloads/ --download all
-##   find tools/busco/test-data/test-db/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
+##   find tools/busco/test-data/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
-##   find tools/busco/test-data/test-db/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
+##   find tools/busco/test-data/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
-##   find tools/busco/test-data/test-db/busco_downloads/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
+##   find tools/busco/test-data/busco_downloads/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
 ##   ```
 ## - test containerized (note: test-data is mounted ro in containerized tests)
 ##
 ## alternatively .. a bit weaker
 ## - set the `test` parameters to `""` comment --offline
 #else:
 --metaeuk
 #end if
 #end if
-#if $outputs and 'image' in $outputs:
+#if $lineage.lineage_mode != "auto_detect":
-&& mkdir BUSCO_summaries
+&& cp busco_galaxy/run_*/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
-&& cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
+&& cp busco_galaxy/run_*/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
-&& generate_plot.py -wd BUSCO_summaries -rt specific
+#if $outputs and 'image' in $outputs:
-#end if
+&& mkdir BUSCO_summaries
+&& cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
-#if $outputs and 'gff' in $outputs:
+&& generate_plot.py -wd BUSCO_summaries -rt specific
-&& echo "\##gff-version 3" > busco_output.gff
+&& cp BUSCO_summaries/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
-## gff files can be absent
+#end if
-&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true)
-#end if
+#if $outputs and 'gff' in $outputs:
-#if $outputs and 'faa' in $outputs:
+&& echo "\##gff-version 3" > busco_galaxy/busco_output.gff
-&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_output.faa 2> /dev/null || true)
+## gff files can be absent
-#end if
+&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
-#if $outputs and 'fna' in $outputs:
+#end if
-&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_output.fna 2> /dev/null || true)
+#if $outputs and 'faa' in $outputs:
+&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
+#end if
+#if $outputs and 'fna' in $outputs:
+&& (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
+#end if
+#end if
+## if $lineage.lineage_mode == "auto_detect", BUSCO output several files with the same name, causing an issue, we need to rename the files
+#if $lineage.lineage_mode == "auto_detect":
+	&& specific_lineage=\$(find ./busco_galaxy -name "short_summary.specific.*.txt" | head -n 1 | cut -d'.' -f4)
+&& generic_lineage=\$(find ./busco_galaxy -name "short_summary.generic.*.txt" | head -n 1 | cut -d'.' -f4)
+	##Rename the output files to differenciate specific and generic lineages results
+## Full table
+&& cp busco_galaxy/run_\${specific_lineage}/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
+&& cp busco_galaxy/run_\${generic_lineage}/full_table.tsv busco_galaxy/full_table_generic_lineage.tsv
+##Missing busco list
+&& cp busco_galaxy/run_\${specific_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
+&& cp busco_galaxy/run_\${generic_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_generic_lineage.tsv
+#if $outputs and 'image' in $outputs:
+&& mkdir BUSCO_summaries_specific
+&& cp busco_galaxy/short_summary.specific.*.txt BUSCO_summaries_specific/
+&& generate_plot.py -wd BUSCO_summaries_specific -rt specific
+&& cp BUSCO_summaries_specific/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
+&& mkdir BUSCO_summaries_generic
+&& cp busco_galaxy/short_summary.generic.*.txt BUSCO_summaries_generic/
+&& generate_plot.py -wd BUSCO_summaries_generic -rt generic
+&& cp BUSCO_summaries_generic/busco_figure.png busco_galaxy/busco_figure_generic_lineage.png
+#end if
+#if $outputs and 'gff' in $outputs:
+## gff files can be absent
+&& echo "\##gff-version 3" > busco_galaxy/busco_output_specific.gff
+&& (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
+&& echo "\##gff-version 3" > busco_galaxy/busco_output_generic.gff
+&& (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_generic.gff 2> /dev/null || true)
+#end if
+#if $outputs and 'faa' in $outputs:
+&& (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
+&& (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_generic.faa 2> /dev/null || true)
+#end if
+#if $outputs and 'fna' in $outputs:
+&& (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
+&& (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_generic.fna 2> /dev/null || true)
+#end if
 #end if
 ]]></command>
 <inputs>
 <param name="test" type="hidden"/>
 <param type="data" name="input" format="fasta,fasta.gz" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."/>
 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
 </param>
+<param name="generic_results" type="boolean" checked="false" label="Do you want to display the results from the generic lineage" help="BUSCO generates files for the parent lineage (generic) and the final selected lineage (specific). Generally, the lineage to select for your assessments should be the most specific lineage available. The generic lineage datasets for the domains archaea, bacteria and eukaryota."/>
 </when>
 <when value="select_lineage">
 <param argument="--lineage_dataset" type="select" label="Lineage">
 <options from_data_table="busco_database_options">
 <filter type="param_value" column="2" ref="cached_db"/>
 </param>
 </when>
 </conditional>
 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
-<option value="short_summary" selected="true">short summary text</option>
+<option value="short_summary" selected="true">Short summary text</option>
-<option value="missing">list with missing IDs</option>
+<option value="missing">List with missing IDs</option>
-<option value="image">summary image</option>
+<option value="image">Summary image</option>
 <option value="gff">gff</option>
 <option value="faa">Protein sequences</option>
 <option value="fna">Nucleotide sequences</option>
 </param>
 <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 ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
+<data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: Short summary - Specific lineage" from_work_dir="busco_galaxy/short_summary.specific.*.txt">
 <filter>outputs and 'short_summary' in outputs</filter>
 </data>
-<data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
+<data name='busco_sum_generic' format='txt' label="${tool.name} on ${on_string}: Short summary - Generic lineage" from_work_dir="busco_galaxy/short_summary.generic.*.txt">
-<data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
+<filter>(outputs and 'short_summary' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: Full table - Specific lineage" from_work_dir="busco_galaxy/full_table_specific_lineage.tsv">
+</data>
+<data name='busco_table_generic' format='tabular' label="${tool.name} on ${on_string}: Full table - Generic lineage" from_work_dir="busco_galaxy/full_table_generic_lineage.tsv">
+<filter>lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: Missing buscos - Specific lineage" from_work_dir="busco_galaxy/missing_busco_list_specific_lineage.tsv">
 <filter>outputs and 'missing' in outputs</filter>
 </data>
-<data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
+<data name='busco_missing_generic' format='tabular' label="${tool.name} on ${on_string}: Missing buscos - Generic lineage" from_work_dir="busco_galaxy/missing_busco_list_generic_lineage.tsv">
+<filter>(outputs and 'missing' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='summary_image' format='png' label="${tool.name} on ${on_string}: Summary image - Specific lineage" from_work_dir="busco_galaxy/busco_figure_specific_lineage.png">
 <filter>outputs and 'image' in outputs</filter>
 </data>
-<data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
+<data name='summary_image_generic' format='png' label="${tool.name} on ${on_string}: Summary image - Generic lineage" from_work_dir="busco_galaxy/busco_figure_generic_lineage.png">
+<filter>(outputs and 'image' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.gff">
 <filter>outputs and 'gff' in outputs</filter>
 </data>
-<data name='busco_faa' format='fasta' label="${tool.name} on ${on_string}: Protein sequences" from_work_dir="busco_output.faa">
+<data name='busco_gff_generic' format='gff3' label="${tool.name} on ${on_string}: GFF - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.gff">
+<filter>(outputs and 'gff' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='busco_faa' format='fasta' label="${tool.name} on ${on_string}: Protein sequences - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.faa">
 <filter>outputs and 'faa' in outputs</filter>
 </data>
-<data name='busco_fna' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences" from_work_dir="busco_output.fna">
+<data name='busco_faa_generic' format='fasta' label="${tool.name} on ${on_string}: Protein sequences - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.faa">
+<filter>(outputs and 'faa' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
+</data>
+<data name='busco_fna' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences - Specific lineage" from_work_dir="busco_galaxy/busco_output_specific.fna">
 <filter>outputs and 'fna' in outputs</filter>
+</data>
+<data name='busco_fna_generic' format='fasta' label="${tool.name} on ${on_string}: Nucleotide sequences - Generic lineage" from_work_dir="busco_galaxy/busco_output_generic.fna">
+<filter>(outputs and 'fna' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']</filter>
 </data>
 </outputs>
 <tests>
 <!-- <test expect_num_outputs="6">
 <param name="test" value="true"/>
 	        <param name="input" value="genome.fa.gz" ftype="fasta.gz"/>
 <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
 <assert_stdout>
 <has_text text="BUSCO analysis done"/>
 </assert_stdout>
 </test> -->
-<test expect_num_outputs="5">
+		<test expect_num_outputs="2">
+<param name="test" value="true"/>
+<param name="input" value="bacilli_odb_test.fasta"/>
+<conditional name="lineage">
+<param name="lineage_mode" value="auto_detect"/>
+<param name="auto_lineage" value="--auto-lineage-prok"/>
+</conditional>
+<conditional name="busco_mode">
+<param name="mode" value="geno"/>
+</conditional>
+<param name="outputs" value="short_summary"/>
+<output name="busco_sum">
+<assert_contents>
+<has_text text="Gene predictor used: prodigal"/>
+</assert_contents>
+</output>
+<output name="busco_table">
+<assert_contents>
+<has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+<has_text text="The lineage dataset is: bacilli_odb10"/>
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="10">
 <param name="test" value="true"/>
 <param name="input" value="genome.fa"/>
 <conditional name="lineage">
 <param name="lineage_mode" value="auto_detect"/>
 <param name="auto_lineage" value="--auto-lineage"/>
+<param name="generic_results" value="true"/>
 </conditional>
 <conditional name="busco_mode">
 <param name="mode" value="geno"/>
 <conditional name="use_augustus">
 <param name="use_augustus_selector" value="metaeuk"/>
 </conditional>
 </conditional>
 <param name="outputs" value="short_summary,missing,image,gff"/>
 <output name="busco_sum">
 <assert_contents>
-<has_text text="Gene predictor used: metaeuk"/>
+<has_text text="Gene predictor used: prodigal"/>
+</assert_contents>
+</output>
+			<output name="busco_sum_generic">
+<assert_contents>
+<has_text text="Gene predictor used: prodigal"/>
 </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"/>
+<has_text text="The lineage dataset is: "/>
 </assert_contents>
 </output>
-<output name="busco_missing">
+<output name="busco_table_generic">
 <assert_contents>
 <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
-<has_text text="The lineage dataset is: eukaryota_odb10"/>
+<has_text text="The lineage dataset is: "/>
+</assert_contents>
+</output>
+			<output name="busco_missing">
+<assert_contents>
+<has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+<has_text text="The lineage dataset is: "/>
+</assert_contents>
+</output>
+			<output name="busco_missing_generic">
+<assert_contents>
+<has_text text="# BUSCO version is: @TOOL_VERSION@"/>
+<has_text text="The lineage dataset is: "/>
 </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"/>
+<output name="summary_image_generic" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
+<output name="busco_gff">
+<assert_contents>
+<has_text text="##gff-version 3"/>
+</assert_contents>
+</output>
+<output name="busco_gff_generic">
+<assert_contents>
+<has_text text="##gff-version 3"/>
+</assert_contents>
+</output>
 <assert_stdout>
 <has_text text="BUSCO analysis done"/>
 </assert_stdout>
 </test>
 <!-- <test expect_num_outputs="3">

Mercurial > repos > iuc > busco

comparison busco.xml @ 22:5dd4f18b0d96 draft default tip