Mercurial > repos > iuc > jbrowse
comparison jbrowse-fromdir.xml @ 35:3235aeb45c22 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
author | iuc |
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date | Wed, 18 Dec 2019 10:46:52 -0500 |
parents | 1cfc579079a6 |
children | 8774b28235bb |
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34:9de82b4963e6 | 35:3235aeb45c22 |
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5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 ## Create output directory | 8 ## Create output directory |
9 mkdir -p $output.files_path && | 9 mkdir -p $output.files_path && |
10 | |
11 export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse && | |
12 | |
10 ## Copy in jbrowse | 13 ## Copy in jbrowse |
11 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ && | 14 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ && |
12 | 15 |
13 ## Copy in data directory | 16 ## Copy in data directory |
14 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ && | 17 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ && |
15 mv $output.files_path/index.html $output | 18 cp $output.files_path/index.html $output |
16 ]]></command> | 19 ]]></command> |
17 <inputs> | 20 <inputs> |
18 <param label="JBrowse Data Directory" | 21 <param label="JBrowse Data Directory" |
19 name="input" | 22 name="input" |
20 type="data" | 23 type="data" |