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comparison busco.xml @ 6:1e62c28ba91d draft

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"planemo upload commit 768639889e24aecd31d85d37d6f0bba00ac2a486"
author iuc
date Wed, 04 Dec 2019 13:45:35 -0500
parents 1440ae06552f
children 4048d82f0c88
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5:1440ae06552f 6:1e62c28ba91d
1 <tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@+galaxy2">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>assess genome assembly and annotation completeness</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.0.2</token> 4 <token name="@TOOL_VERSION@">3.0.2</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
8 <requirement type="package" version="3.5.1">r-base</requirement> 8 <requirement type="package" version="3.5.1">r-base</requirement>
9 <requirement type="package" version="3.3.2">augustus</requirement> 9 <requirement type="package" version="3.3.2">augustus</requirement>
10 <requirement type="package" version="1.29">tar</requirement>
10 </requirements> 11 </requirements>
11 <command><![CDATA[ 12 <command><![CDATA[
12 export BUSCO_CONFIG_FILE='busco_config.ini' && 13 export BUSCO_CONFIG_FILE='busco_config.ini' &&
13 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && 14 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
14 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && 15 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
15 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 16 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
16 17
17 #if $adv.aug_prediction.augustus_mode == 'history': 18 #if $adv.aug_prediction.augustus_mode == 'history':
18 ## Using an augustus model from history, we need to unzip it and let augustus find it 19 ## Using an augustus model from history, we need to unzip it and let augustus find it
19 mkdir -p 'augustus_dir/species/' && 20 mkdir -p 'augustus_dir/species/' &&
20 tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null && 21 tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' &&
21 #end if 22 #end if
22 23
23 run_BUSCO.py 24 run_BUSCO.py
24 --in '${input}' 25 --in '${input}'
25 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' 26 --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}'