Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt
diff eurl_vtec_wgs_pt.xml @ 0:965517909457 draft
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
| author | cstrittmatter |
|---|---|
| date | Wed, 22 Jan 2020 08:41:44 -0500 |
| parents | |
| children | bf3194a789a2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eurl_vtec_wgs_pt.xml Wed Jan 22 08:41:44 2020 -0500 @@ -0,0 +1,201 @@ +<tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3"> + <description>performs various typing tools + </description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package">scipy</requirement> + <requirement type="package">perl-bioperl</requirement> + <requirement type="package" version="2.2.9">bowtie2</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> + <requirement type="package" version="1.3.1">bcftools</requirement> + <requirement type="package">bwa</requirement> + <requirement type="package">blast</requirement> + <requirement type="package">spades</requirement> + <requirement type="package">fastqc</requirement> + <requirement type="package">mentalist</requirement> + </requirements> + <!-- basic error handling --> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command> + python + $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci + #if str( $library.type ) == "single": + -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' + --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} + --text1 $text_file_1 --trimmed1 $trimmed1 + #elif str( $library.type ) == "paired": + -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' + --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} + --text1 $text_file_1 --trimmed1 $trimmed1 + -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}' + --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} + --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired + #elif str( $library.type ) == "pairedcollection": + -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}' + --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} + --text1 $text_file_1 --trimmed1 $trimmed1 + -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}' + --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} + --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired + #end if + #if $serotyping: + --serotyping + --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_H + #end if + #if $virulotyping: + --virulotyping + --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id) + #end if + #if $shigatoxintyping: + --shigatoxintyping + --blastn_STX $blastn_STX + #end if + </command> + + <inputs> + <!-- single/paired --> + <conditional name="library"> + <param name="type" type="select" label="Is this a single-end or paired-end library"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="pairedcollection">Paired-end collection</option> + </param> + <when value="single"> + <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> + </when> + <when value="paired"> + <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> + <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> + </when> + <when value="pairedcollection"> + <param name="input_pc" type="data_collection" label="Paired-end FASTQ collection" help="Must be of datatype "fastqsanger"" optional="false" format="txt" collection_type="paired" /> + </when> + </conditional> + <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" /> + <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" /> + <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" /> + </inputs> + + <!-- define outputs --> + <outputs> + <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" /> + <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" /> + <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true"> + <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> + </data> + <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true"> + <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> + </data> + <data name="trimmed1" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed + #if str( $library.type ) == 'paired'# + forward + #end if# + FASTQ"> + </data> + <data name="trimmed2" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed reverse FASTQ"> + <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> + </data> + <data name="trimmedunpaired" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed unpaired reads"> + <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> + </data> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> + <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true"> + <filter>virulotyping</filter> + </data> + <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" > + <filter>shigatoxintyping</filter> + </data> + <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" /> + <data name="spades_log" format="txt" label="SPAdes log" hidden="true"> + <filter>serotyping</filter> + </data> + <data name="blastn_O" format="tabular" label="Blastn for O on ${on_string}" hidden="true"> + <filter>serotyping</filter> + </data> + <data name="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true"> + <filter>serotyping</filter> + </data> + <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data> + </outputs> + + <tests> + <test> + <!-- basic test on contigs file --> + <param name="type" value="single"/> + <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/> + <param name="serotyping" value="true"/> + <output name="report_out"> + <assert_contents> + <has_text text="wzx_208_AF529080_O26" /> + <has_text text="wzy_192_AF529080_O26" /> + <has_text text="fliC_269_AY337465_H11" /> + <has_text text="fliC_276_AY337472_H11" /> + </assert_contents> + </output> + <output name="blastn_O" file="blastn_O" ftype="tabular" /> + <output name="blastn_H" file="blastn_H" ftype="tabular" /> + </test> + </tests> + + <help> +**EURL VTEC WGS PT Overview** +This tool performs various typing tools: + +- Raw data quality check (FASTQC) + +- Trimming (FASTQ positional and quality trimming) + +- Virulotyping (patho_typing tool from the INNUENDO Project) + +- Multi Locus Sequence Typing (MentaLiST 7 loci) + +- Filtering (DUK) + +- Assembly (SPAdes) + +- Serotyping (blastn) + +- Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU) + +Istituto Superiore di Sanità + +European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) + +Developer: Arnold Knijn arnold.knijn@iss.it + +The development of the Virulotyping tool has 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 +("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento” +from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014) +[FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)]. + </help> + <citations> + <citation type="bibtex">@ARTICLE{andrews_s, + author = {Andrews, S}, + keywords = {bioinformatics, ngs, qc}, + title = {{FastQC A Quality Control tool for High Throughput Sequence Data}}, + url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/} + }</citation> + <citation type="doi">10.1093/bioinformatics/btu135</citation> + <citation type="doi">10.1186/gb-2009-10-3-r25</citation> + <citation type="doi">10.1038/nmeth.1923</citation> + <citation type="doi">10.1099/mgen.0.000146</citation> + <citation type="bibtex">@ARTICLE{li-copeland, + author = {Li, M, Copeland, A, and Han, J}, + keywords = {bioinformatics, ngs}, + title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}}, + url = {https://www.osti.gov/servlets/purl/1016000/} + }</citation> + <citation type="bibtex">@ARTICLE{edwards_ra, + author = {Edwards, RA}, + keywords = {bioinformatics, ngs}, + title = {{fastq-pair}}, + url = {https://github.com/linsalrob/EdwardsLab/} + }</citation> + <citation type="doi">10.1089/cmb.2012.0021</citation> + <citation type="doi">10.1186/1471-2105-10-421</citation> + <citation type="doi">10.1186/s13742-015-0080-7</citation> + <citation type="doi">10.1128/JCM.00008-15</citation> + </citations> +</tool>