Mercurial > repos > thanhlv > socru
comparison socru.xml @ 1:a7ccd6b0788e draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/socru commit 1024f378b83203ab9c365a7d386981ad257ce1d1-dirty
| author | thanhlv |
|---|---|
| date | Thu, 07 Feb 2019 16:43:41 -0500 |
| parents | fcb4d9f67e75 |
| children | 435f1b59e064 |
comparison
equal
deleted
inserted
replaced
| 0:fcb4d9f67e75 | 1:a7ccd6b0788e |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="version_command" /> | 7 <expand macro="version_command" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 | |
| 10 #set $_input_file = "'{}'".format($assembly.element_identifier) | |
| 11 ln -s '${assembly}' ${_input_file} && | |
| 12 | |
| 9 socru | 13 socru |
| 10 | 14 |
| 11 --threads \${GALAXY_SLOTS:-4} | 15 --threads \${GALAXY_SLOTS:-4} |
| 12 | 16 |
| 13 --top_blast_hits top_blast_hits.tsv | 17 --top_blast_hits top_blast_hits.tsv |
| 14 | 18 |
| 15 #if str($opt_args.max_bases_from_ends) != "" | 19 #if str($opt_args.max_bases_from_ends) != "" |
| 16 --max_bases_from_ends $max_bases_from_ends | 20 --max_bases_from_ends $$opt_args.max_bases_from_ends |
| 17 #end if | 21 #end if |
| 18 | 22 |
| 19 --not_circular $opt_args.not_circular | 23 --not_circular $opt_args.not_circular |
| 20 --min_bit_score $opt_args.min_bit_score | 24 --min_bit_score $opt_args.min_bit_score |
| 21 --min_alignment_length $opt_args.min_alignment_length | 25 --min_alignment_length $opt_args.min_alignment_length |
| 22 | 26 |
| 23 #if $opt_args.verbose | 27 #if $opt_args.verbose |
| 24 $opt_args.verbose | 28 $opt_args.verbose |
| 25 #end if | 29 #end if |
| 26 $species $assembly | 30 $species ${_input_file} |
| 27 > $output | 31 > $output |
| 28 ]]></command> | 32 ]]></command> |
| 29 | 33 |
| 30 <inputs> | 34 <inputs> |
| 31 <param name="assembly" type="data" format="fasta" label="Select fasta dataset" help=""/> | 35 <param name="assembly" type="data" format="fasta" label="Select fasta dataset" help=""/> |