comparison jbrowse2/jbrowse2.xml @ 10:0db895a99532 draft default tip

Uploaded

9:6a41f87b5d7f

    <command detect_errors="aggressive"><![CDATA[
mkdir -p '$output.files_path' &&
## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp '$trackxml' '$output.files_path/galaxy.xml' &&

export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse))/../opt/jbrowse2  &&

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse2.py'

--jbrowse \${JBROWSE_SOURCE_DIR}

--outdir '$output.files_path'
'$trackxml' &&

cp '$output.files_path/index.html' '$output'

## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
#if str($uglyTestingHack) == "enabled":

10:0db895a99532

    <command detect_errors="aggressive"><![CDATA[
mkdir -p '$output.files_path' &&
## Copy the XML file into the directory, mostly for debugging
## but nice if users want to reproduce locally
cp '$trackxml' '$output.files_path/galaxy.xml' &&
export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse)) &&
## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse2.py'
--jbrowse \${JBROWSE_SOURCE_DIR}
--outdir '$output.files_path'
--xml '$trackxml' &&

cp '$output.files_path/index.html' '$output'

## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
#if str($uglyTestingHack) == "enabled":