| Previous changeset 1:093352878303 (2019-05-03) |
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Commit message:
Update to xml file |
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modified:
chewbbaca.xml |
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| diff -r 093352878303 -r 872ed5ee7b98 chewbbaca.xml --- a/chewbbaca.xml Fri May 03 10:15:27 2019 -0400 +++ b/chewbbaca.xml Fri May 10 07:04:48 2019 -0400 |
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| b'@@ -1,305 +1,304 @@\n-<tool id="chewBBACA" name="chewBBACA" version="2.0">\n- <description>BSR-Based Allele Calling Algorithm\n- </description>\n- <requirements>\n- <requirement type="package" version="3.6">Python</requirement>\n- <requirement type="package" version="1.15.3">numpy</requirement>\n- <requirement type="package" version="0.19.1">scipy</requirement>\n- <requirement type="package" version="5.22.2.1">perl</requirement>\n- <requirement type="package" version="1.72">biopython</requirement>\n- <requirement type="package" version="3.8.1">plotly</requirement>\n- <requirement type="package" version="1.8.2">SPARQLWrapper</requirement>\n- <requirement type="package" version="0.23.4">pandas</requirement>\n- <requirement type="package" version="2.5.0">blast</requirement>\n- <requirement type="package" version="2.6.3">prodigal</requirement>\n- <requirement type="package" version="2.1">clustalw</requirement>\n- <requirement type="package" version="7.313">mafft</requirement>\n- <requirement type="package" version="2.0.16">chewbbaca</requirement>\n- </requirements>\n- <!-- basic error handling -->\n- <stdio>\n- <!-- Assume anything other than zero is an error -->\n- <exit_code range="1:" level="fatal" description="Tool exception" />\n- <exit_code range=":-1" level="fatal" description="Tool exception" />\n- </stdio>\n- <command>\n- perl \n- $__tool_directory__/chewBBACA.pl $selectFunction.myFunctions\n- #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n- \'${",".join(map(str, $selectFunction.input1))}\'\n- #elif str( $selectFunction.myFunctions ) in (\'SchemaEvaluator\', \'TestGenomeQuality\', \'ExtractCgMLST\', \'RemoveGenes\')\n- $selectFunction.input1\n- #else\n- \'NULL\'\n- #end if\n- #if str( $selectFunction.myFunctions ) == \'AlleleCall\'\n- #set $input_names = []\n- #for $input in $selectFunction.input1\n- $input_names.append($input.element_identifier)\n- #end for\n- #set $input_name = ",".join(map(str, $input_names))\n- \'$input_name\'\n- #else\n- \'NULL\'\n- #end if\n- #if str( $selectFunction.myFunctions ) == \'CreateSchema\'\n- \'$schema\'\n- #elif str( $selectFunction.myFunctions ) == \'AlleleCall\'\n- \'$statistics,$contigsinfo,$alleles,$logginginfo,$repeatedloci\'\n- #elif str( $selectFunction.myFunctions ) == \'SchemaEvaluator\'\n- \'$schemaplot\'\n- #elif str( $selectFunction.myFunctions ) == \'TestGenomeQuality\'\n- \'$thresholdplot,$removedgenomes\'\n- #elif str( $selectFunction.myFunctions ) == \'RemoveGenes\'\n- \'$removedgenes\'\n- #else\n- \'NULL\'\n- #end if\n-\n- "chewBBACA.py $selectFunction.myFunctions\n- #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\', \'TestGenomeQuality\', \'ExtractCgMLST\')\n- -o output_dir\n- #end if\n- #if str( $selectFunction.myFunctions ) == \'RemoveGenes\'\n- -o output_removegenes\n- #end if\n- #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n- -i input_dir\n- --cpu \\${GALAXY_SLOTS:-4}\n- #end if\n- #if str( $selectFunction.myFunctions ) in (\'SchemaEvaluator\', \'TestGenomeQuality\', \'ExtractCgMLST\', \'RemoveGenes\')\n- -i $selectFunction.input1\n- #end if\n- #if str( $selectFunction.myFunctions ) in (\'CreateSchema\', \'AlleleCall\')\n- #if $selectFunction.bsr\n- --bsr $selectFunction.bsr\n- #end if\n-\n- #if $selectFunction.ptfmode.ptf_select=="system"\n- --ptf ${ filter( lambda x: str( x[0] ) == str( $selectFunction.ptfmode.ptf_system ), $__app__.tool_data_tables[ \'chew'..b'or"</filter>\r\n+ </data>\r\n+ <data format="html" name="thresholdplot" from_work_dir="output_dir/GenomeQualityPlot.html" label="${tool.name}:TestGenomeQuality on ${on_string}: Plot" >\r\n+ <filter>selectFunction[\'myFunctions\'] == "TestGenomeQuality"</filter>\r\n+ </data>\r\n+ <data format="tsv" name="removedgenomes" from_work_dir="output_dir/removedGenomes.txt" label="${tool.name}:TestGenomeQuality on ${on_string}: Removed genomes" >\r\n+ <filter>selectFunction[\'myFunctions\'] == "TestGenomeQuality"</filter>\r\n+ </data>\r\n+ <data format="tsv" name="cgmlst" from_work_dir="output_dir/cgMLST.tsv" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLST" >\r\n+ <filter>selectFunction[\'myFunctions\'] == "ExtractCgMLST"</filter>\r\n+ </data>\r\n+ <data format="txt" name="cgmlstschema" from_work_dir="output_dir/cgMLSTschema.txt" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLSTschema" >\r\n+ <filter>selectFunction[\'myFunctions\'] == "ExtractCgMLST"</filter>\r\n+ </data>\r\n+ <data format="tsv" name="removedgenes" from_work_dir="output_removegenes.tsv" label="${tool.name}:RemoveGenes on ${on_string}" >\r\n+ <filter>selectFunction[\'myFunctions\'] == "RemoveGenes"</filter>\r\n+ </data>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test>\r\n+ <param name="selectFunction[\'myFunctions\']" value="AlleleCall" />\r\n+ <param name="input1" value="a_contigs.fasta" ftype="fasta" />\r\n+ <param name="selectFunction.mode[\'schema_select\']" value="system" />\r\n+ <param name="selectFunction.mode[\'reference\']" value="schema_pubMLST" />\r\n+ <param name="selectFunction.mode[\'ptf_select\']" value="noptf" />\r\n+ <output name="statistics" >\r\n+ <assert_contents>\r\n+ <has_text text="a_contigs.fasta" />\r\n+ </assert_contents>\r\n+\t\t\t</output>\r\n+ </test>\r\n+ </tests>\r\n+ <help>\r\n+**chewBBACA** stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow" \r\n+but at this point still it needs a bit of work to make that claim so we just add "chew" to add extra coolness to the software name.\r\n+\r\n+The development of the tools have been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2\r\n+("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - \xe2\x80\x9cFundos Europeus Estruturais e de Investimento\xe2\x80\x9d \r\n+from \xe2\x80\x9cPrograma Operacional Regional Lisboa 2020\xe2\x80\x9d and by national funds from FCT - \xe2\x80\x9cFunda\xc3\xa7\xc3\xa3o para a Ci\xc3\xaancia e a Tecnologia\xe2\x80\x9d and BacGenTrack (TUBITAK/0004/2014) \r\n+[FCT/ Scientific and Technological Research Council of Turkey (T\xc3\xbcrkiye Bilimsel ve Teknolojik Ara\xc5\x9frrma Kurumu, T\xc3\x9cBITAK)].\r\n+ </help>\r\n+ <citations>\r\n+ <citation type="bibtex">@ARTICLE{andrews_s,\r\n+ author = {Rossi, M and Silva, M and Ribeiro-Gon\xc3\xa7alves, 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,\r\n+ J and Jaakkonen, A and Palma, F and Culebro, A and Kivist\xc3\xb6, R and H\xc3\xa4nninen, ML and Laukkanen-Ninios, R and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M and Garaizer, J and Bikandi, J and Hilbert,\r\n+ F and Taboada, EN and Carri\xc3\xa7o, JA},\r\n+ keywords = {bioinformatics, ngs, mlst},\r\n+ title = {{INNUENDO whole and core genome MLST databases and schemas for foodborne pathogens}},\r\n+ url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}\r\n+ }</citation>\r\n+ <citation type="doi">10.1099/mgen.0.000166</citation>\r\n+ <citation type="doi">10.1371/journal.pgen.1007261</citation>\r\n+ </citations>\r\n+</tool>\r\n' |