Mercurial > repos > dfornika > chewbbaca_allelecall
changeset 0:42858df73d3b draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
| author | dfornika |
|---|---|
| date | Fri, 24 Jan 2020 00:12:19 +0000 |
| parents | |
| children | 624f77d91a11 |
| files | chewbbaca_allelecall.xml macros.xml |
| diffstat | 2 files changed, 79 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chewbbaca_allelecall.xml Fri Jan 24 00:12:19 2020 +0000 @@ -0,0 +1,76 @@ +<tool id="chewbbaca_allelecall" name="chewBBACA AlleleCall" version="@TOOL_VERSION@+galaxy0"> + <description>BSR-Based Allele Calling Algorithm</description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + chewBBACA.py AlleleCall + --threads \${GALAXY_SLOTS:-1} + -i '${assembly}' + --bsr '${min_bsr}' + --st '${size_threshold}' + ]]> + </command> + + <inputs> + <conditional name="prodigal_training_file_source"> + <param name="prodigal_training_file_source_selector" type="select" + label="Select a Prodigal training file from your history or use one from a tool data table?"> + <option value="No" selected="true">No Prodigal training file</option> + <option value="tool_data_table">Prodigal training file from tool data table</option> + <option value="history">Prodigal training file from history</option> + </param> + <when value="No"/> + <when value="tool_data_table"> + <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> + <options from_data_table="chewbbaca_prodigal_training_files"> + <validator type="no_options" message="No chewBBACA prodigal training files are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="prodigal_training_file" type="data" format="binary" + label="Prodigal training file" + help=""/> + </when> + </conditional> + <param name="assembly" format="fasta" type="data" label="Genome assembly (fasta)" /> + <param name="min_bsr" type="float" value="0.6" optional="true" label="minimum BSR score" /> + <param name="size_threshold" type="float" min="0.0" value="0.2" max="1.0" optional="true" label="Size threshold" /> + </inputs> + + <!-- define outputs --> + <outputs> + <data format="tabular" name="statistics" label="${tool.name}: on ${on_string}: Statistics" /> + <data format="tabular" name="contigs_info" label="${tool.name}: on ${on_string}: Contigs Info" /> + <data format="tabular" name="alleles" label="${tool.name}: on ${on_string}: Alleles" /> + <data format="txt" name="log" label="${tool.name}: on ${on_string}: Log" /> + <data format="tabular" name="repeated_loci" label="${tool.name}: on ${on_string}: Repeated Loci" /> + </outputs> + <tests> + + </tests> + <help><![CDATA[ + ]]> + </help> + <citations> + <citation type="bibtex"> + @ARTICLE{andrews_s, + author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN + and Machado, MP and Oleastro, M and Borges, V and Isidro, J + and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK + and Halkilahti, J and Jaakkonen, A and Palma, F and Culebro, A + and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R + and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M + and Garaizer, J and Bikandi, J and Hilbert, F and Taboada, EN + and Carriço, JA}, + keywords = {bioinformatics, ngs, mlst}, + title = {{INNUENDO whole and core genome MLST databases and schemas + for foodborne pathogens}}, + url = {https://github.com/TheInnuendoProject/chewBBACA_schemas} + } + </citation> + <citation type="doi">10.1099/mgen.0.000166</citation> + <citation type="doi">10.1371/journal.pgen.1007261</citation> + </citations> +</tool>