| Previous changeset 12:1278204240d8 (2021-11-02) Next changeset 14:e4bd1e99bacf (2022-04-05) |
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Commit message:
"planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b" |
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modified:
busco.xml macros.xml |
| b |
| diff -r 1278204240d8 -r 46ae58b1d792 busco.xml --- a/busco.xml Tue Nov 02 09:40:29 2021 +0000 +++ b/busco.xml Fri Nov 05 08:41:35 2021 +0000 |
| [ |
| @@ -49,7 +49,7 @@ #end if #end if -#if $adv.outputs and 'image' in $adv.outputs: +#if $outputs and 'image' in $outputs: && mkdir BUSCO_summaries && @@ -119,26 +119,27 @@ </when> </conditional> + <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> + <option value="short_summary" selected="true">short summary text</option> + <option value="missing">list with missing IDs</option> + <option value="image">summary image</option> + </param> + <section name="adv" title="Advanced Options" expanded="False"> <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> - <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> - <option value="short_summary">short summary text</option> - <option value="missing">list with missing IDs</option> - <option value="image">summary image</option> - </param> </section> </inputs> <outputs> <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> - <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter> + <filter>outputs and 'short_summary' in outputs</filter> </data> <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"> - <filter>adv['outputs'] and 'missing' in adv['outputs']</filter> + <filter>outputs and 'missing' in outputs</filter> </data> <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> - <filter>adv['outputs'] and 'image' in adv['outputs']</filter> + <filter>outputs and 'image' in outputs</filter> </data> </outputs> <tests> @@ -154,9 +155,7 @@ <param name="use_augustus_selector" value="yes" /> </conditional> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing" /> - </section> + <param name="outputs" value="short_summary,missing" /> <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> <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"> @@ -174,9 +173,7 @@ <conditional name="busco_mode"> <param name="mode" value="prot" /> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing,image" /> - </section> + <param name="outputs" value="short_summary,missing,image" /> <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" /> <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" /> @@ -191,9 +188,7 @@ <conditional name="busco_mode"> <param name="mode" value="tran" /> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing,image" /> - </section> + <param name="outputs" value="short_summary,missing,image" /> <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> <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" /> @@ -215,9 +210,7 @@ </conditional> </conditional> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary" /> - </section> + <param name="outputs" value="short_summary" /> <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> </test> @@ -237,9 +230,7 @@ </conditional> </conditional> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing" /> - </section> + <param name="outputs" value="short_summary,missing" /> <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> <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" /> @@ -256,9 +247,7 @@ <param name="use_augustus_selector" value="no" /> </conditional> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing,image" /> - </section> + <param name="outputs" value="short_summary,missing,image" /> <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" /> @@ -276,9 +265,7 @@ <param name="use_augustus_selector" value="no" /> </conditional> </conditional> - <section name="adv"> - <param name="outputs" value="short_summary,missing,image" /> - </section> + <param name="outputs" value="short_summary,missing,image" /> <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="4" /> <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" /> <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" /> |
| b |
| diff -r 1278204240d8 -r 46ae58b1d792 macros.xml --- a/macros.xml Tue Nov 02 09:40:29 2021 +0000 +++ b/macros.xml Fri Nov 05 08:41:35 2021 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">5.2.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="citations"> <citations> @@ -14,7 +14,6 @@ <option value="human">Homo sapiens</option> <option value="fly">Drosophila melanogaster</option> <option value="arabidopsis">Arabidopsis thaliana</option> - <option value="brugia ">Brugia malayi</option> <option value="aedes">Aedes aegypti</option> <option value="tribolium2012">Tribolium castaneum</option> <option value="schistosoma">Schistosoma mansoni</option> @@ -22,41 +21,38 @@ <option value="galdieria">Galdieria sulphuraria</option> <option value="maize">Zea mays</option> <option value="toxoplasma">Toxoplasma gondii</option> - <option value="caenorhabditis ">Caenorhabditis elegans</option> + <option value="caenorhabditis">Caenorhabditis elegans</option> <option value="aspergillus_fumigatus">Aspergillus fumigatus</option> - <option value="aspergillus_nidulans ">Aspergillus nidulans</option> - <option value="aspergillus_oryzae ">Aspergillus oryzae</option> + <option value="aspergillus_nidulans">Aspergillus nidulans</option> + <option value="aspergillus_oryzae">Aspergillus oryzae</option> <option value="aspergillus_terreus">Aspergillus terreus</option> - <option value="botrytis_cinerea ">Botrytis cinerea</option> - <option value="candida_albicans ">Candida albicans</option> - <option value="candida_guilliermondii ">Candida guilliermondii</option> - <option value="candida_tropicalis ">Candida tropicalis</option> + <option value="botrytis_cinerea">Botrytis cinerea</option> + <option value="candida_albicans">Candida albicans</option> + <option value="candida_guilliermondii">Candida guilliermondii</option> + <option value="candida_tropicalis">Candida tropicalis</option> <option value="chaetomium_globosum">Chaetomium globosum</option> <option value="coccidioides_immitis">Coccidioides immitis</option> - <option value="coprinus">Coprinus cinereus</option> <option value="coprinus_cinereus">Coprinus cinereus</option> <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option> - <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option> - <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option> - <option value="cryptococcus">Cryptococcus neoformans</option> + <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans B</option> + <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans JEC21</option> <option value="debaryomyces_hansenii">Debaryomyces hansenii</option> <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option> <option value="eremothecium_gossypii">Eremothecium gossypii</option> - <option value="fusarium_graminearum ">Fusarium graminearum</option> - <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option> - <option value="histoplasma">Histoplasma capsulatum</option> - <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option> - <option value="laccaria_bicolor ">Laccaria bicolor</option> + <option value="fusarium_graminearum">Fusarium graminearum</option> + <option value="histoplasma_capsulatum">Histoplasma capsulatum</option> + <option value="kluyveromyces_lactis">Kluyveromyces lactis</option> + <option value="laccaria_bicolor">Laccaria bicolor</option> <option value="lamprey">Petromyzon marinus</option> <option value="leishmania_tarentolae">Leishmania tarentolae</option> <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option> - <option value="magnaporthe_grisea ">Magnaporthe grisea</option> + <option value="magnaporthe_grisea">Magnaporthe grisea</option> <option value="neurospora_crassa">Neurospora crassa</option> <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> <option value="pichia_stipitis">Pichia stipitis</option> <option value="rhizopus_oryzae">Rhizopus oryzae</option> - <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option> - <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option> + <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae S288C</option> + <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae rm11-1a_1</option> <option value="saccharomyces">Saccharomyces cerevisiae</option> <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option> <option value="trichinella">Trichinella spiralis</option> @@ -79,20 +75,16 @@ <option value="thermoanaerobacter_tengcongensis">Thermoanaerobacter tengcongensis</option> <option value="wheat">wheat</option> <option value="zebrafish">Danio rerio</option> - <option value="anidulans">Aspergillus nidulans</option> <option value="bombus_impatiens1">Bombus impatiens1</option> <option value="bombus_terrestris2">Bombus terrestris2</option> - <option value="botrytis_cinerea">Botrytis cinerea</option> <option value="brugia_malayi">Brugia malayi</option> <option value="conidiobolus_coronatus">Conidiobolus coronatus</option> <option value="cryptococcus_neoformans">Cryptococcus neoformans</option> <option value="culex_pipiens">Culex pipiens</option> <option value="elephant_shark">Callorhinchus milii</option> <option value="honeybee1">Apis mellifera</option> - <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option> <option value="pea_aphid">Acyrthosiphon pisum</option> <option value="rhodnius_prolixus">Rhodnius prolixus</option> - <option value="ustilago_maydis">Ustilago maydis</option> <option value="verticillium_albo_atrum1">Verticillium albo atrum1</option> <option value="verticillium_longisporum1">Verticillium longisporum1</option> <option value="Xipophorus_maculatus">Xipophorus_maculatus</option> |