comparison bbmerge.xml @ 3:82ced0e47b9d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c

2:6d084528a6f1

    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
    #set read2_file = $read2_identifier + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

bbmerge.sh
#### Input parameters
#if str($input_type_cond.input_type) == 'single':
    in='${read1_file}'
    interleaved=t
#else:

3:82ced0e47b9d

    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
    #set read2_file = $read2_identifier + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
    export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
fi &&

bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"

#### Input parameters
#if str($input_type_cond.input_type) == 'single':
    in='${read1_file}'
    interleaved=t
#else: