Mercurial > repos > dvanzessen > bcbio_nextgen_emc

comparison bcbio-nextgen.xml @ 3:cb60ea3f8f62 draft

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author dvanzessen
date Mon, 22 Jul 2019 04:59:16 -0400
parents 34eab86b26ba
children 7211d3a78fe0
comparison
equal deleted inserted replaced
2:34eab86b26ba 3:cb60ea3f8f62
1 <tool id="bcbio-nextgen" name="BCBio" version="0.1.0"> 1 <tool id="bcbio-nextgen" name="BCBio" version="0.1.0">
2 <command detect_errors="exit_code"><![CDATA[ 2 <command detect_errors="exit_code"><![CDATA[
3 PATH="/bcbio/tool_dir/bin:/bcbio/anaconda/bin:\$PATH" && 3 PATH="\$BCBIO_DIRECTORY/tool_dir/bin:\$BCBIO_DIRECTORY/anaconda/bin:\$PATH" &&
4 mkdir $everything_else.files_path && 4 mkdir $everything_else.files_path &&
5 cd $everything_else.files_path && 5 cd $everything_else.files_path &&
6 python $__tool_directory__/script.py --workdir `pwd` --output-dir `pwd`/output --template $main --output-conf `pwd`/config.yaml 6 python $__tool_directory__/script.py --workdir `pwd` --output-dir `pwd`/output --template $main --output-conf `pwd`/config.yaml
7 #if str( $region_file.has_region_file_select ) == "yes": 7 #if str( $region_file.has_region_file_select ) == "yes":
8 --bed ${region_file.bed} 8 --bed ${region_file.bed}
9 #end if 9 #end if
10 #for $i, $sample in enumerate( $samples ) 10 #for $i, $sample in enumerate( $samples )
11 --input $sample.forward:$sample.reverse:$sample.phenotype 11 --input $sample.forward:$sample.reverse:$sample.phenotype
12 #end for 12 #end for
13 && bcbio_nextgen.py /bcbio/galaxy/bcbio_system.yaml `pwd`/config.yaml && 13 && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml &&
14 zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf && 14 zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
15 python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else 15 python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else
16 ]]></command> 16 ]]></command>
17 <configfiles> 17 <configfiles>
18 <configfile name='main'> 18 <configfile name='main'>