changeset 4:5ecdeca79a0d draft

planemo upload commit a91c8bf878080b84ef938e1f95217c6bf3f0cba1

--- a/busco.xml	Fri Dec 14 08:13:25 2018 -0500
+++ b/busco.xml	Thu Feb 21 14:33:28 2019 -0500
@@ -1,45 +1,42 @@
-<tool id="busco" name="Busco" version="3.0.2">
+<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy0">
     <description>assess genome assembly and annotation completeness</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.0.2</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="3.0.2">busco</requirement>
-        <requirement type="package" version="2.2.1">r-ggplot2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
+        <requirement type="package" version="3.5.1">r-base</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 &&
-        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
-        export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+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 &&
+cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
 
-        #if $adv.aug_prediction.augustus_mode == 'history':
-            ## Using an augustus model from history, we need to unzip it and let augustus find it
-
-            mkdir -p 'augustus_dir/species/' &&
-
-            tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
-        #end if
+#if $adv.aug_prediction.augustus_mode == 'history':
+    ## Using an augustus model from history, we need to unzip it and let augustus find it
+    mkdir -p 'augustus_dir/species/' &&
+    tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
+#end if
 
-        run_BUSCO.py
-        --in '${input}'
-        --lineage_path '${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 $adv.aug_prediction.augustus_mode == 'builtin':
-            --species '${adv.aug_prediction.augustus_species}'
-        #else if $adv.aug_prediction.augustus_mode == 'history':
-            --species local
-        #end if
-        --tarzip
+run_BUSCO.py
+--in '${input}'
+--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 $adv.aug_prediction.augustus_mode == 'builtin':
+    --species '${adv.aug_prediction.augustus_species}'
+#else if $adv.aug_prediction.augustus_mode == 'history':
+    --species local
+#end if
+--tarzip
     ]]></command>
 
     <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>
@@ -224,11 +221,10 @@
         </test>
     </tests>
     <help>
-        BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
+BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
 
-        .. _BUSCO: http://busco.ezlab.org/
+.. _BUSCO: http://busco.ezlab.org/
     </help>
-
      <citations>
         <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>
     </citations>