comparison jbrowse-fromdir.xml @ 35:3235aeb45c22 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"

34:9de82b4963e6

  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
## Create output directory
mkdir -p $output.files_path &&
## Copy in jbrowse
cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&

## Copy in data directory
cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
mv $output.files_path/index.html $output
]]></command>
  <inputs>
    <param label="JBrowse Data Directory"
           name="input"
           type="data"

35:3235aeb45c22

  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code"><![CDATA[
## Create output directory
mkdir -p $output.files_path &&

export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse  &&

## Copy in jbrowse
cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&

## Copy in data directory
cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
cp $output.files_path/index.html $output
]]></command>
  <inputs>
    <param label="JBrowse Data Directory"
           name="input"
           type="data"