diff busco.xml @ 2:382a4c19007f draft

planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e

--- a/busco.xml	Tue Jan 24 12:08:38 2017 -0500
+++ b/busco.xml	Fri Oct 20 03:54:35 2017 -0400
@@ -1,22 +1,39 @@
-<tool id="busco" name="Busco" version="2.0">
+<tool id="busco" name="Busco" version="3.0.2">
     <description>assess genome assembly and annotation completeness</description>
-
     <requirements>
-        <requirement type="package" version="2.0">busco</requirement>
+        <requirement type="package" version="3.0.2">busco</requirement>
+        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
     </requirements>
+    <command><![CDATA[
+        export BUSCO_CONFIG_FILE='busco_config.ini'
 
-    <command><![CDATA[
-        BUSCO.py
+        &&
+
+        #if $adv.aug_prediction.augustus_mode == 'history':
+            ## Using an augustus model from history, we need to unzip it and let augustus find it
+
+            cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+
+            mkdir -p 'augustus_dir/species/' &&
+
+            tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
+
+            export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+        #end if
+
+        run_BUSCO.py
         --in '${input}'
-        --lineage '${lineage.fields.path}'
+        --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'
         --mode '${mode}'
         -o "busco_galaxy"
         --cpu \${GALAXY_SLOTS:-4}
         --evalue ${adv.evalue}
         ${adv.long}
         --limit ${adv.limit}
-        #if $adv.species:
-            --species '${adv.species}'
+        #if $adv.aug_prediction.augustus_mode == 'builtin':
+            --species '${adv.aug_prediction.augustus_species}'
+        #else if $adv.aug_prediction.augustus_mode == 'history':
+            --species local
         #end if
         --tarzip
     ]]></command>
@@ -24,14 +41,13 @@
     <inputs>
 
         <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
-
         <param argument="--mode" type="select" label="Mode">
             <option value="geno">Genome</option>
             <option value="tran">Transcriptome</option>
             <option value="prot">Proteome</option>
         </param>
 
-        <param argument="--lineage" type="select" label="Lineage">
+        <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" />
@@ -41,7 +57,118 @@
         <section name="adv" title="Advanced Options" expanded="False">
             <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
             <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
-            <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/>
+
+            <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>
+                    <option value="builtin">Use another predefined species model</option>
+                    <option value="history">Use a custom species model</option>
+                </param>
+                <when value="no"/>
+                <when value="history">
+                    <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
+                </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>
+                    </param>
+                </when>
+            </conditional>
             <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
         </section>
     </inputs>
@@ -53,7 +180,7 @@
     <tests>
         <test>
             <param name="input" value="genome.fa"/>
-            <param name="lineage" value="arthropoda_2.0"/>
+            <param name="lineage_path" value="arthropoda"/>
             <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"/>
@@ -61,7 +188,7 @@
         </test>
         <test>
             <param name="input" value="proteome.fa"/>
-            <param name="lineage" value="arthropoda_2.0"/>
+            <param name="lineage_path" value="arthropoda"/>
             <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"/>
@@ -69,12 +196,32 @@
         </test>
         <test>
             <param name="input" value="transcriptome.fa"/>
-            <param name="lineage" value="arthropoda_2.0"/>
+            <param name="lineage_path" value="arthropoda"/>
             <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"/>
             <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
         </test>
+        <test>
+            <param name="input" value="genome.fa"/>
+            <param name="lineage_path" value="arthropoda"/>
+            <param name="mode" value="geno"/>
+            <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
+            <param name="adv|aug_prediction|augustus_species" value="human"/>
+            <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"/>
+        </test>
+        <test>
+            <param name="input" value="genome.fa"/>
+            <param name="lineage_path" value="arthropoda"/>
+            <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"/>
+            <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"/>
+        </test>
     </tests>
     <help>
         BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs