Mercurial > repos > thanhlv > socru
changeset 5:602f0fe854a3 draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/socru commit bba783a0821434deae678830e7e07c947cbe6b8e-dirty
| author | thanhlv |
|---|---|
| date | Thu, 23 May 2019 04:59:27 -0400 |
| parents | bf0efbba5e8d |
| children | a6d085138f56 |
| files | socru.xml |
| diffstat | 1 files changed, 8 insertions(+), 6 deletions(-) [+] |
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--- a/socru.xml Fri May 17 11:19:28 2019 -0400 +++ b/socru.xml Thu May 23 04:59:27 2019 -0400 @@ -6,10 +6,12 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ - - #set $_input_file = "'{}'".format($assembly.element_identifier) - ln -s '${assembly}' ${_input_file} && - + #import re + #import os.path + + #set $_input_file = re.sub(r'(\s|\(|\)|:|!)', '_', str($assembly.element_identifier)) + ln -s '${assembly}' $_input_file && + socru --threads \${GALAXY_SLOTS:-4} @@ -21,7 +23,7 @@ #end if #if $opt_args.not_circular - --not_circular + $opt_args.not_circular #end if --min_bit_score $opt_args.min_bit_score @@ -35,7 +37,7 @@ ]]></command> <inputs> - <param name="assembly" type="data" format="fasta" label="Select fasta dataset" help=""/> + <param name="assembly" type="data" format="fasta,fasta.gz" label="Select fasta dataset" help=""/> <param name="species" type="select" label="Select a species" > <option value="Acetobacter_ascendens">Acetobacter_ascendens</option> <option value="Acetobacter_pasteurianus">Acetobacter_pasteurianus</option>