| Previous changeset 15:41030a6c03b7 (2022-04-11) Next changeset 17:e824f5d958d0 (2023-03-02) |
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Commit message:
planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe |
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modified:
busco.xml macros.xml test-data/genome_results/full_table test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/genome_results_metaeuk/full_table test-data/genome_results_metaeuk/missing_buscos_list test-data/genome_results_metaeuk/short_summary test-data/genome_results_metaeuk/summary.png test-data/genome_results_metaeuk_auto/full_table test-data/genome_results_metaeuk_auto/missing_buscos_list test-data/genome_results_metaeuk_auto/short_summary test-data/genome_results_metaeuk_auto/summary.png test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/proteome_results/summary.png test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/short_summary test-data/transcriptome_results/summary.png |
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added:
test-data/genome_results_metaeuk/out.gff test-data/genome_results_metaeuk_auto/out.gff test-data/transcriptome_results/out.gff |
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| diff -r 41030a6c03b7 -r bb935709506a busco.xml --- a/busco.xml Mon Apr 11 09:02:11 2022 +0000 +++ b/busco.xml Thu Jan 12 13:28:58 2023 +0000 |
| [ |
| b'@@ -1,11 +1,11 @@\n <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>assess genome assembly and annotation completeness</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n <xrefs>\n <xref type="bio.tools">busco</xref>\n </xrefs>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">busco</requirement>\n <requirement type="package" version="1.34">tar</requirement>\n@@ -13,16 +13,21 @@\n </requirements>\n <version_command>busco --version</version_command>\n <command><![CDATA[\n+\n+#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\':\n+\n if [ -z "\\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\\$(dirname \\$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\\$(realpath \\${BUSCO_PATH}/../config) ; fi &&\n cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n \n-#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\' and $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n+#if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n ## Using an augustus model from history, we need to unzip it and let augustus find it\n mkdir -p \'augustus_dir/species/\' &&\n tar -C \'augustus_dir/species/\' -xzf \'${busco_mode.use_augustus.aug_prediction.augustus_model}\' &&\n #end if\n \n+#end if\n+\n busco\n --in \'${input}\'\n --update-data\n@@ -59,6 +64,14 @@\n generate_plot.py -wd BUSCO_summaries -rt specific\n #end if\n \n+#if $outputs and \'gff\' in $outputs:\n+ &&\n+ echo "\\##gff-version 3" > busco_output.gff\n+ &&\n+ ## gff files can be absent\n+ cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true\n+#end if\n+\n ]]> </command>\n <inputs>\n <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />\n@@ -123,6 +136,7 @@\n <option value="short_summary" selected="true">short summary text</option>\n <option value="missing">list with missing IDs</option>\n <option value="image">summary image</option>\n+ <option value="gff">gff</option>\n </param>\n \n <section name="adv" title="Advanced Options" expanded="False">\n@@ -141,9 +155,12 @@\n <data name=\'summary_image\' format=\'png\' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">\n <filter>outputs and \'image\' in outputs</filter>\n </data>\n+ <data name=\'busco_gff\' format=\'gff3\' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">\n+ <filter>outputs and \'gff\' in outputs</filter>\n+ </data>\n </outputs>\n <tests>\n- <test expect_num_outputs="3">\n+ <test expect_num_outputs="4">\n <param name="input" value="genome.fa" />\n <conditional name="lineage">\n <param name="lineage_mode" value="select_lineage" />\n@@ -155,16 +172,22 @@\n <param name="use_augustus_selector" value="yes" />\n </conditional>\n </conditional>\n- <param name="outputs" value="short_summary,missing" />\n+ <param name="outputs" value="short_summary,missing,gff" />\n <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />\n <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />\n+ <output name="busco_gff">\n+ <assert_contents>\n+ <has_n_lines n="1"/>\n+ <has_text text="##gff-version 3" />\n+ </assert_contents>\n+ </output>\n <out'..b'scriptome_results/full_table" compare="diff" lines_diff="6" />\n <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />\n <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />\n+ <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />\n </test>\n- <test expect_num_outputs="2">\n+ <test expect_num_outputs="3">\n <param name="input" value="genome.fa" />\n <conditional name="lineage">\n <param name="lineage_mode" value="select_lineage" />\n@@ -210,9 +240,15 @@\n </conditional>\n </conditional>\n </conditional>\n- <param name="outputs" value="short_summary" />\n+ <param name="outputs" value="short_summary,gff" />\n <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />\n <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />\n+ <output name="busco_gff">\n+ <assert_contents>\n+ <has_n_lines n="1"/>\n+ <has_text text="##gff-version 3" />\n+ </assert_contents>\n+ </output>\n </test>\n <test expect_num_outputs="3">\n <param name="input" value="genome.fa" />\n@@ -235,7 +271,7 @@\n <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />\n <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />\n </test>\n- <test expect_num_outputs="4">\n+ <test expect_num_outputs="5">\n <param name="input" value="genome.fa" />\n <conditional name="lineage">\n <param name="lineage_mode" value="select_lineage" />\n@@ -247,13 +283,14 @@\n <param name="use_augustus_selector" value="no" />\n </conditional>\n </conditional>\n- <param name="outputs" value="short_summary,missing,image" />\n+ <param name="outputs" value="short_summary,missing,image,gff" />\n <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />\n <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />\n <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />\n <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />\n+ <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />\n </test>\n- <test expect_num_outputs="4">\n+ <test expect_num_outputs="5">\n <param name="input" value="genome.fa" />\n <conditional name="lineage">\n <param name="lineage_mode" value="auto_detect" />\n@@ -265,11 +302,12 @@\n <param name="use_augustus_selector" value="no" />\n </conditional>\n </conditional>\n- <param name="outputs" value="short_summary,missing,image" />\n+ <param name="outputs" value="short_summary,missing,image,gff" />\n <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />\n <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />\n <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />\n <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />\n+ <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />\n </test>\n </tests>\n <help><
