Mercurial > repos > thanhlv > socru
comparison socru.xml @ 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 |
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| 4:bf0efbba5e8d | 5:602f0fe854a3 |
|---|---|
| 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 | 9 #import re |
| 10 #set $_input_file = "'{}'".format($assembly.element_identifier) | 10 #import os.path |
| 11 ln -s '${assembly}' ${_input_file} && | 11 |
| 12 | 12 #set $_input_file = re.sub(r'(\s|\(|\)|:|!)', '_', str($assembly.element_identifier)) |
| 13 ln -s '${assembly}' $_input_file && | |
| 14 | |
| 13 socru | 15 socru |
| 14 | 16 |
| 15 --threads \${GALAXY_SLOTS:-4} | 17 --threads \${GALAXY_SLOTS:-4} |
| 16 | 18 |
| 17 --top_blast_hits top_blast_hits.tsv | 19 --top_blast_hits top_blast_hits.tsv |
| 19 #if str($opt_args.max_bases_from_ends) != "" | 21 #if str($opt_args.max_bases_from_ends) != "" |
| 20 --max_bases_from_ends $opt_args.max_bases_from_ends | 22 --max_bases_from_ends $opt_args.max_bases_from_ends |
| 21 #end if | 23 #end if |
| 22 | 24 |
| 23 #if $opt_args.not_circular | 25 #if $opt_args.not_circular |
| 24 --not_circular | 26 $opt_args.not_circular |
| 25 #end if | 27 #end if |
| 26 | 28 |
| 27 --min_bit_score $opt_args.min_bit_score | 29 --min_bit_score $opt_args.min_bit_score |
| 28 --min_alignment_length $opt_args.min_alignment_length | 30 --min_alignment_length $opt_args.min_alignment_length |
| 29 | 31 |
| 33 $species ${_input_file} | 35 $species ${_input_file} |
| 34 > $output | 36 > $output |
| 35 ]]></command> | 37 ]]></command> |
| 36 | 38 |
| 37 <inputs> | 39 <inputs> |
| 38 <param name="assembly" type="data" format="fasta" label="Select fasta dataset" help=""/> | 40 <param name="assembly" type="data" format="fasta,fasta.gz" label="Select fasta dataset" help=""/> |
| 39 <param name="species" type="select" label="Select a species" > | 41 <param name="species" type="select" label="Select a species" > |
| 40 <option value="Acetobacter_ascendens">Acetobacter_ascendens</option> | 42 <option value="Acetobacter_ascendens">Acetobacter_ascendens</option> |
| 41 <option value="Acetobacter_pasteurianus">Acetobacter_pasteurianus</option> | 43 <option value="Acetobacter_pasteurianus">Acetobacter_pasteurianus</option> |
| 42 <option value="Achromobacter_denitrificans">Achromobacter_denitrificans</option> | 44 <option value="Achromobacter_denitrificans">Achromobacter_denitrificans</option> |
| 43 <option value="Achromobacter_insolitus">Achromobacter_insolitus</option> | 45 <option value="Achromobacter_insolitus">Achromobacter_insolitus</option> |