# HG changeset patch
# User abretaud
# Date 1453132355 18000
# Node ID a8ddf9d3c14ca50345a05e2b7f9cb8af580cd55c
# Parent  13981b0bc0cbaebf330d5b57cddb6f52a0e9e780
Uploaded

diff -r 13981b0bc0cb -r a8ddf9d3c14c busco.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/busco.xml	Mon Jan 18 10:52:35 2016 -0500
@@ -0,0 +1,97 @@
+<tool id="busco" name="Busco" version="1.1b1">
+    <description>assess genome assembly and annotation completeness</description>
+
+    <requirements>
+        <requirement type="package" version="1.1b1">busco</requirement>
+        <requirement type="package" version="3.1">augustus</requirement>
+        <requirement type="package" version="2.2.31">blast+</requirement>
+        <requirement type="package" version="3.1b2">hmmer</requirement>
+        <requirement type="package" version="3.4">python</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command><![CDATA[
+        python3 \${BUSCO_ROOT_PATH}/BUSCO.py
+        -in "${input}"
+        -l "\${BUSCO_DATA_PATH}/${lineage}"
+        -m "${mode}"
+        -o "busco_galaxy"
+        -c \${GALAXY_SLOTS:-4}
+        -ev ${adv.ev}
+        ${adv.long}
+        #if ($adv.flank):
+            -flank ${adv.flank}
+        #end if
+        -sp ${adv.species}
+    ]]></command>
+    
+    <inputs>
+    
+        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
+    
+        <param name="lineage" type="select" label="Lineage">
+            <option value="arthropoda">Arthropoda</option>
+            <option value="bacteria">Bacteria</option>
+            <option value="eukaryota">Eukaryota</option>
+            <option value="fungi">Fungi</option>
+            <option value="metazoa">Metazoa</option>
+            <option value="vertebrata">Vertebrata</option>
+        </param>
+    
+        <param name="mode" type="select" label="Mode">
+            <option value="all">Genome</option>
+            <option value="trans">Transcriptome</option>
+            <option value="OGS">Proteome</option>
+        </param>
+        
+        <section name="adv" title="Advanced Options" expanded="False">
+            <param name="ev" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
+            <param name="flank" type="integer" value="" optional="True" label="Flanking sequence size for candidate regions" help="If not provided, flank size is calculated based on genome size with a range from 5 to 20 Kbp."/>
+            <param name="species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/>
+            <param name="long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds ~20h extra run time, but can improve results for some non-model organisms"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy"/>
+        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy"/>
+        <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_buscos_list_busco_galaxy"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="genome.fa"/>
+            <param name="lineage" value="arthropoda"/>
+            <param name="mode" value="all"/>
+            <output name="busco_sum" file="genome_results/short_summary" compare="contains"/>
+            <output name="busco_table" file="genome_results/full_table" compare="contains"/>
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="contains"/>
+        </test>
+        <test>
+            <param name="input" value="proteome.fa"/>
+            <param name="lineage" value="arthropoda"/>
+            <param name="mode" value="OGS"/>
+            <output name="busco_sum" file="proteome_results/short_summary" compare="contains"/>
+            <output name="busco_table" file="proteome_results/full_table" compare="contains"/>
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="contains"/>
+        </test>
+        <test>
+            <param name="input" value="transcriptome.fa"/>
+            <param name="lineage" value="arthropoda"/>
+            <param name="mode" value="trans"/>
+            <output name="busco_sum" file="transcriptome_results/short_summary" compare="contains"/>
+            <output name="busco_table" file="transcriptome_results/full_table" compare="contains"/>
+            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+        BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
+        
+        .. _BUSCO: http://busco.ezlab.org/
+    </help>
+    
+     <citations>
+        <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
+    </citations>
+</tool>