Mercurial > repos > genouest > logol
comparison logol.xml @ 1:08a6fd2620b3 draft default tip
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit d89aeeba8550252ef3231f433856950ce921f9cd
| author | genouest |
|---|---|
| date | Thu, 07 Jun 2018 05:24:36 -0400 |
| parents | f11370aba286 |
| children |
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| 0:f11370aba286 | 1:08a6fd2620b3 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="logol_wrapper" name="Logol" version="1.7.8"> | 2 <tool id="logol_wrapper" name="Logol" version="1.7.8"> |
| 3 <description>Biological patterns matching</description> | 3 <description>Biological patterns matching</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="1.7.8=1">logol</requirement> | 5 <requirement type="package" version="1.7.8">logol</requirement> |
| 6 <requirement type="package" version="6.0">unzip</requirement> | 6 <requirement type="package" version="6.0">unzip</requirement> |
| 7 </requirements> | 7 </requirements> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 | 9 |
| 10 ## generate properties file | 10 ## generate properties file |
| 66 <option value="rna">RNA</option> | 66 <option value="rna">RNA</option> |
| 67 <option value="protein">PROTEIN</option> | 67 <option value="protein">PROTEIN</option> |
| 68 </param> | 68 </param> |
| 69 | 69 |
| 70 <param argument="-s" type="data" format="fasta" label="Read from file" help="Fasta sequence to analyse" /> | 70 <param argument="-s" type="data" format="fasta" label="Read from file" help="Fasta sequence to analyse" /> |
| 71 | |
| 72 <param argument="-max" type="integer" value="100" label="Maximum number of result matches"/> | 71 <param argument="-max" type="integer" value="100" label="Maximum number of result matches"/> |
| 73 <param argument="-fasta" type="boolean" truevalue="-fasta" falsevalue="" label="Add fasta conversion to result archive" checked="False" value="False"/> | 72 <param argument="-fasta" type="boolean" truevalue="-fasta" falsevalue="" label="Add fasta conversion to result archive" checked="False" value="False"/> |
| 74 <param argument="-gff" type="boolean" truevalue="-gff" falsevalue="" label="Add gff conversion to result archive" checked="False" value="False"/> | 73 <param argument="-gff" type="boolean" truevalue="-gff" falsevalue="" label="Add gff conversion to result archive" checked="False" value="False"/> |
| 75 <param argument="-all" type="boolean" truevalue="-all" falsevalue="" label="Search sequence in both directions" checked="False" value="False"/> | 74 <param argument="-all" type="boolean" truevalue="-all" falsevalue="" label="Search sequence in both directions" checked="False" value="False"/> |
| 76 <param argument="-maxmatchsize" type="integer" value="0" label="Maximum size of a match (0 is no limit)"/> | 75 <param argument="-maxmatchsize" type="integer" value="0" label="Maximum size of a match (0 is no limit)"/> |
| 77 <param argument="-maxspacer" type="integer" value="0" label="Maximum size of a spacer (0 is no limit)"/> | 76 <param argument="-maxspacer" type="integer" value="0" label="Maximum size of a spacer (0 is no limit)"/> |
| 78 <param argument="-lmax" type="integer" value="0" label="Maximum size of a word (0 is no limit)"/> | 77 <param argument="-lmax" type="integer" value="0" label="Maximum size of a word (0 is no limit)"/> |
| 79 <param argument="-lmin" type="integer" value="2" label="Minimum size of a word"/> | 78 <param argument="-lmin" type="integer" value="2" label="Minimum size of a word"/> |
| 80 <param argument="-forcesplit" truevalue="-forcesplit" falsevalue="" type="boolean" label="Allow sequence cut (if several models are defined in rule, all models will look for pattern in same sequence range" checked="False" value="False"/> | 79 <param argument="-forcesplit" truevalue="-forcesplit" falsevalue="" type="boolean" label="Allow sequence cut (if several models are defined in rule, all models will look for pattern in same sequence range" checked="False" value="False"/> |
| 81 <param name="zip" type="boolean" label="Generate zip archive with all files" checked="False" value="False" help="Zip file contains all xml and fasta/gff files if conversion is activated"/> | 80 <param name="zip" type="boolean" label="Generate zip archive with all files" checked="False" value="False" help="Zip file contains all xml and fasta/gff files if conversion is activated"/> |
| 82 | |
| 83 </inputs> | 81 </inputs> |
| 84 <outputs> | 82 <outputs> |
| 85 <data format="txt" name="log_file" label="Log : ${tool.name} on ${on_string}" /> | 83 <data format="txt" name="log_file" label="Log : ${tool.name} on ${on_string}" /> |
| 86 <data format="zip" name="logol_results_archive" from_work_dir="logol_results.zip" label="Compressed files : ${tool.name} on ${on_string}"> | 84 <data format="zip" name="logol_results_archive" from_work_dir="logol_results.zip" label="Compressed files : ${tool.name} on ${on_string}"> |
| 87 <filter>zip</filter> | 85 <filter>zip</filter> |