diff busco.xml @ 7:4048d82f0c88 draft

"planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c"

--- a/busco.xml	Wed Dec 04 13:45:35 2019 -0500
+++ b/busco.xml	Mon Aug 17 06:50:18 2020 -0400
@@ -1,17 +1,14 @@
-<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@+galaxy2">
+<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">
     <description>assess genome assembly and annotation completeness</description>
     <macros>
-        <token name="@TOOL_VERSION@">3.0.2</token>
+        <import>macros.xml</import>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
-        <requirement type="package" version="3.5.1">r-base</requirement>
-        <requirement type="package" version="3.3.2">augustus</requirement>
-        <requirement type="package" version="1.29">tar</requirement>
+        <requirement type="package" version="1.32">tar</requirement>
     </requirements>
     <command><![CDATA[
-export BUSCO_CONFIG_FILE='busco_config.ini' &&
-if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
+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/ &&
 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
 
@@ -21,9 +18,10 @@
     tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' &&
 #end if
 
-run_BUSCO.py
+busco
 --in '${input}'
---lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
+--lineage_dataset '${lineage_dataset}'
+--update-data
 --mode '${mode}'
 -o busco_galaxy
 --cpu \${GALAXY_SLOTS:-4}
@@ -31,11 +29,10 @@
 ${adv.long}
 --limit ${adv.limit}
 #if $adv.aug_prediction.augustus_mode == 'builtin':
-    --species '${adv.aug_prediction.augustus_species}'
+    --augustus_species '${adv.aug_prediction.augustus_species}'
 #else if $adv.aug_prediction.augustus_mode == 'history':
-    --species local
+    --augustus_species local
 #end if
---tarzip
     ]]></command>
 
     <inputs>
@@ -46,11 +43,8 @@
             <option value="prot">Proteome</option>
         </param>
 
-        <param argument="--lineage_path" type="select" label="Lineage">
-            <options from_data_table="busco">
-                <filter type="sort_by" column="2" />
-                <validator type="no_options" message="No indexes are available" />
-            </options>
+        <param argument="--lineage_dataset" type="select" label="Lineage">
+            <expand macro="lineages"/>
         </param>
 
         <section name="adv" title="Advanced Options" expanded="False">
@@ -69,102 +63,7 @@
                 </when>
                 <when value="builtin">
                     <param name="augustus_species" type="select" label="Augustus species model">
-                        <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->
-                        <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>
-                        <option value="tetrahymena">Tetrahymena thermophila</option>
-                        <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="aspergillus_fumigatus">Aspergillus fumigatus</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="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="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="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="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">Saccharomyces cerevisiae</option>
-                        <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>
-                        <option value="trichinella">Trichinella spiralis</option>
-                        <option value="ustilago_maydis">Ustilago maydis</option>
-                        <option value="yarrowia_lipolytica">Yarrowia lipolytica</option>
-                        <option value="nasonia">Nasonia vitripennis</option>
-                        <option value="tomato">Solanum lycopersicum</option>
-                        <option value="chlamydomonas">Chlamydomonas reinhardtii</option>
-                        <option value="amphimedon">Amphimedon queenslandica</option>
-                        <option value="pneumocystis">Pneumocystis jirovecii</option>
-                        <option value="chicken">Gallus gallus domesticus (chicken)</option>
-                        <option value="cacao">Theobroma cacao (cacao)</option>
-                        <option value="heliconius_melpomene1">Heliconius melpomene</option>
-                        <option value="xenoturbella">Xenoturbella</option>
-                        <option value="E_coli_K12">E coli K12</option>
-                        <option value="c_elegans_trsk">c elegans trsk</option>
-                        <option value="camponotus_floridanus">Camponotus floridanus</option>
-                        <option value="coyote_tobacco">Coyote tobacco</option>
-                        <option value="s_aureus">Staphylococcus aureus</option>
-                        <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>
-                        <option value="adorsata">adorsata</option>
-                        <option value="ancylostoma_ceylanicum">ancylostoma_ceylanicum</option>
-                        <option value="maker2_athal1">maker2_athal1</option>
-                        <option value="maker2_c_elegans1">maker2_c_elegans1</option>
-                        <option value="maker2_dmel1">maker2_dmel1</option>
-                        <option value="maker2_spomb1">maker2_spomb1</option>
-                        <option value="parasteatoda">parasteatoda</option>
-                        <option value="rice">rice</option>
-                        <option value="schistosoma2">schistosoma2</option>
-                        <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>
+                        <expand macro="augustus_species"/>
                     </param>
                 </when>
             </conditional>
@@ -172,14 +71,14 @@
         </section>
     </inputs>
     <outputs>
-        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>
-        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>
-        <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>
+        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"/>
+        <data name='busco_table' format='tabular' label="${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"/>
     </outputs>
     <tests>
         <test>
             <param name="input" value="genome.fa"/>
-            <param name="lineage_path" value="arthropoda"/>
+            <param name="lineage_dataset" value="arthropoda_odb10"/>
             <param name="mode" value="geno"/>
             <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"/>
@@ -187,7 +86,7 @@
         </test>
         <test>
             <param name="input" value="proteome.fa"/>
-            <param name="lineage_path" value="arthropoda"/>
+            <param name="lineage_dataset" value="arthropoda_odb10"/>
             <param name="mode" value="prot"/>
             <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"/>
@@ -195,7 +94,7 @@
         </test>
         <test>
             <param name="input" value="transcriptome.fa"/>
-            <param name="lineage_path" value="arthropoda"/>
+            <param name="lineage_dataset" value="arthropoda_odb10"/>
             <param name="mode" value="tran"/>
             <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
             <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
@@ -203,7 +102,7 @@
         </test>
         <test>
             <param name="input" value="genome.fa"/>
-            <param name="lineage_path" value="arthropoda"/>
+            <param name="lineage_dataset" value="arthropoda_odb10"/>
             <param name="mode" value="geno"/>
             <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
             <param name="adv|aug_prediction|augustus_species" value="human"/>
@@ -213,7 +112,7 @@
         </test>
         <test>
             <param name="input" value="genome.fa"/>
-            <param name="lineage_path" value="arthropoda"/>
+            <param name="lineage_dataset" value="arthropoda_odb10"/>
             <param name="mode" value="geno"/>
             <param name="adv|aug_prediction|augustus_mode" value="history"/>
             <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
@@ -227,7 +126,5 @@
 
 .. _BUSCO: http://busco.ezlab.org/
     </help>
-     <citations>
-        <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>