Mercurial > repos > dfornika > chewbbaca_prepexternalschema
diff chewbbaca_prepexternalschema.xml @ 0:68e59c40b1ea draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 6ce8b601276a1161318b908647cc7a4f0af5b91e-dirty"
| author | dfornika |
|---|---|
| date | Tue, 02 Jun 2020 00:23:09 +0000 |
| parents | |
| children | eac851537d92 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chewbbaca_prepexternalschema.xml Tue Jun 02 00:23:09 2020 +0000 @@ -0,0 +1,41 @@ +<tool id="chewbbaca_prepexternalschema" name="chewBBACA PrepExternalSchema" version="@TOOL_VERSION@+galaxy0"> + <description>Adapt an external schema to be used with chewBBACA.</description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + mkdir input_files && + #for $f in in str( $input_fasta ).split(','): + #set $filename = os.path.basename( str($f) ).replace(".dat", "") + ln -s ${f} input_files/${filename}.fasta + chewBBACA.py PrepExternalSchema + --cpu \${GALAXY_SLOTS:-1} + -i 'input_files' + #if str( translation_table ) != "": + --tbl '${translation_table}' + #end if + --bsr '${bsr}' + --len '${len}' + -o schema + && tar -czf schema.tgz schema + ]]> + </command> + <inputs> + <param name="input_fasta" format="fasta" type="data" multiple="true" label="Schema files (fasta)" /> + <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" /> + <param name="min_len" type="integer" min="1" value="100" max="100000" optional="true" label="Minimum length" /> + </inputs> + <outputs> + <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> + <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Alleles" from_work_dir="schema_invalid_alleles.txt"/> + <data name="invalid_alleles" format="txt" label="${tool.name}: on ${on_string}: Invalid Genes" from_work_dir="schema_invalid_genes.txt"/> + <data name="summary_stats" format="txt" label="${tool.name}: on ${on_string}: Summary Stats" from_work_dir="schema_summary_stats.txt"/> + </outputs> + <tests> + + </tests> + <help><![CDATA[ + ]]> + </help> + <expand macro="citations"/> +</tool>