Mercurial > repos > iuc > busco
diff busco.xml @ 21:2babe6d5c561 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a
author | iuc |
---|---|
date | Fri, 30 Aug 2024 15:19:56 +0000 |
parents | ea8146ee148f |
children |
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--- a/busco.xml Mon Mar 18 16:01:49 2024 +0000 +++ b/busco.xml Fri Aug 30 15:19:56 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/ && @@ -40,8 +40,6 @@ #if $lineage_conditional.selector == 'cached': --offline --download_path $lineage_conditional.cached_db.fields.path -#else - --update-data #end if #if $lineage.lineage_mode == "auto_detect": @@ -50,21 +48,20 @@ --lineage_dataset '${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 - #end if -#end if - -#if str( $busco_mode.mode ) == "geno": - #if $busco_mode.miniprot: - --miniprot + #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin': + --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}' + #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': + --augustus_species local + #end if + #else: + --metaeuk #end if #end if @@ -111,14 +108,16 @@ <option value="prot">annotated gene sets (protein)</option> </param> <when value="geno"> - <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> - <option value="yes">Yes, use Augustus</option> - <option value="no" selected="true">Use Metaeuk</option> + <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor"> + <option value="augustus">Augustus</option> + <option value="metaeuk">Metaeuk</option> + <option value="miniprot" selected="true">Miniprot</option> + </param> - <when value="no" /> - <when value="yes"> + <when value="metaeuk"/> + <when value="miniprot"/> + <when value="augustus"> <conditional name="aug_prediction"> <param name="augustus_mode" type="select" label="Augustus species model"> <option value="no" selected="true">Use the default species for selected lineage</option> @@ -189,10 +188,7 @@ </data> <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff"> <filter>outputs and 'gff' in outputs</filter> - </data> - <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff"> - <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter> - </data> + </data> </outputs> <tests> @@ -205,23 +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="re_match_multiline" /> - <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" /> @@ -233,9 +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="re_match_multiline" /> - <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> @@ -254,13 +256,17 @@ <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="re_match_multiline" /> + <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" /> <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="3"> <param name="input" value="genome.fa" /> <conditional name="lineage"> <param name="lineage_mode" value="select_lineage" /> @@ -268,9 +274,8 @@ </conditional> <conditional name="busco_mode"> <param name="mode" value="geno" /> - <param name="miniprot" value="true"/> <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" /> @@ -278,16 +283,18 @@ </conditional> </conditional> <param name="outputs" value="short_summary,gff" /> - <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/> - <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"/> <has_text text="##gff-version 3" /> </assert_contents> </output> - <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. --> - <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/> </test> <test expect_num_outputs="3"> <param name="input" value="genome.fa" /> @@ -298,7 +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" /> @@ -306,9 +313,14 @@ </conditional> </conditional> <param name="outputs" value="short_summary,missing" /> - <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> - <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" /> @@ -319,19 +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="re_match_multiline" /> - <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" ftype="gff3"> + <output name="busco_sum"> <assert_contents> - <has_n_lines n="13"/> + <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" /> @@ -342,32 +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="6" /> - <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[