diff busco.xml @ 0:5e3543b1ef9f draft

planemo upload commit 0de2ff52c643ec5bd6c26110878f2d74405fdf08

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/busco.xml	Thu Jan 12 15:12:47 2017 -0500
@@ -0,0 +1,86 @@
+<tool id="busco" name="Busco" version="2.0">
+    <description>assess genome assembly and annotation completeness</description>
+
+    <requirements>
+        <requirement type="package" version="2.0">busco</requirement>
+    </requirements>
+
+    <command><![CDATA[
+        BUSCO.py
+        --in '${input}'
+        --lineage '${lineage.fields.path}'
+        --mode '${mode}'
+        -o "busco_galaxy"
+        --cpu \${GALAXY_SLOTS:-4}
+        --evalue ${adv.evalue}
+        ${adv.long}
+        --limit ${adv.limit}
+        --species ${adv.species}
+        --tarzip
+    ]]></command>
+
+    <inputs>
+
+        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
+
+        <param argument="--mode" type="select" label="Mode">
+            <option value="geno">Genome</option>
+            <option value="tran">Transcriptome</option>
+            <option value="prot">Proteome</option>
+        </param>
+
+        <param argument="--lineage" type="select" label="Lineage">
+            <options from_data_table="busco">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No indexes are available" />
+            </options>
+        </param>
+
+        <section name="adv" title="Advanced Options" expanded="False">
+            <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
+            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
+            <param argument="--species" type="text" value="generic" label="Name of existing Augustus species gene finding metaparameters"/>
+            <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name='busco_sum' format='txt' label="${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"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="genome.fa"/>
+            <param name="lineage" value="arthropoda_2.0"/>
+            <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"/>
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="input" value="proteome.fa"/>
+            <param name="lineage" value="arthropoda_2.0"/>
+            <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"/>
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="input" value="transcriptome.fa"/>
+            <param name="lineage" value="arthropoda_2.0"/>
+            <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>
+    </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>