Mercurial > repos > nml > cryptogenotyper
view cryptogenotyper.xml @ 0:06afaa20dd23 draft
"planemo upload for repository https://github.com/phac-nml/CryptoGenotyper commit 2754239279293498574292d06f8f77b4a326b177"
author | nml |
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date | Fri, 16 Oct 2020 02:23:24 +0000 |
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children | d4a96287909e |
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<tool id="CryptoGenotyper" name = "CryptoGenotyper" version="@VERSION@"> <description> CryptoGenotyper is a standalone tool to analyze Cryptosporidium Sanger sequencing data and classify the species and subtype based on SSU rRNA and gp60 gene markers, respectively. </description> <macros> <token name="@VERSION@">1.0</token> </macros> <requirements> <requirement type="package" version ="@VERSION@">cryptogenotyper</requirement> </requirements> <version_command>cryptogenotyper --version</version_command> <command detect_errors="exit_code"> <![CDATA[ #set $ref_file='' #if $reference.ref == "no" ln -s "${reference.db}" "${reference.db.name}" && #set $ref_file = $reference.db.name #end if #if $primers["seqtype"] == "contig" ln -s "${$primers.abi_input["forward"]}" "${primers.abi_input.name}_forward.ab1" && ln -s "${$primers.abi_input["reverse"]}" "${primers.abi_input.name}_reverse.ab1" && cryptogenotyper -i "." -m "$marker" -t "$primers.seqtype" -f "forward" -r "reverse" #if $reference.ref == "no" --databasefile $ref_file #end if #else ln -s "${primers.abi_input}" "${primers.abi_input.element_identifier}" && cryptogenotyper -i "./${primers.abi_input.element_identifier}" -m "$marker" -t "$primers.seqtype" -f "" -r "" #if $reference.ref == "no" --databasefile $ref_file #end if #end if #if $outputheader == "no" --noheaderline #end if -o "result"; ]]> </command> <inputs> <param name="marker" type="select" label="Marker"> <option value="18S">SSU rRNA</option> <option value="gp60">gp60</option> </param> <conditional name="reference"> <param name="ref" type="select" label="Use default reference file?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="yes"> </when> <when value="no"> <param name="db" type="data" format="fasta" label="Reference Database File:" help=".fa fasta file type"/> </when> </conditional> <conditional name="primers"> <param name="seqtype" type="select" label="Type of Sequences"> <option value="forward">Forward Only</option> <option value="reverse">Reverse Only</option> <option selected="true" value="contig">Contig</option> </param> <when value="contig"> <param name="abi_input" type="data_collection" collection_type="paired" format="ab1" label="Paired Sequencing File(s)" help=".ab1 file type"/> </when> <when value="forward"> <param name="abi_input" type="data" format="ab1" label="Forward Sequencing File(s)" help=".ab1 file type"/> </when> <when value="reverse"> <param name="abi_input" type="data" format="ab1" label="Reverse Sequencing File(s)" help=".ab1 file type"/> </when> </conditional> <param name="outputheader" type="select" value="yes" label="Output header line in the report?"> <option value="yes">Yes</option> <option value="no">No</option> </param> </inputs> <outputs> <data name="outfile" format="fasta" from_work_dir="result_cryptogenotyper_report.fa" label="${tool.name}:${on_string}:fastas"/> <data name="outfile_report" format="tabular" from_work_dir="result_cryptogenotyper_report.txt" label="${tool.name}:${on_string}:reports"/> </outputs> <tests> <test> <param name="marker" value="18S"/> <param name="seqtype" value="forward"/> <param name="abi_input" value="P17705_Crypto16-2F-20170927_SSUF_G12_084.ab1"/> <output name="outfile_report" ftype="tabular"> <assert_contents> <has_text_matching expression="C.parvum"/> </assert_contents> </output> </test> <test> <param name="marker" value="gp60"/> <param name="seqtype" value="forward"/> <param name="abi_input" value="P17705_gp60-Crypt14-1F-20170927_gp60F_G07_051.ab1"/> <output name="outfile_report" ftype="tabular" > <assert_contents> <has_text_matching expression="C.parvum"/> </assert_contents> </output> </test> </tests> <help> **Syntax** CryptoGenotyper is a standalone tool to *in-silico* determine species and subtype based on SSU rRNA and gp60 markers. For more information please visit https://github.com/phac-nml/CryptoGenotyper. ----- **Input:** AB1 file(s) representing *Cryptosporidium's* SSU rRNA or gp60 locus (forward, reverse, or contig (forward and reverse paired-end reads)). Optional: A custom reference database in .fa file format, to be used during the homology search for *Cryptosporidium* classification. **Output:** FASTA file containing the identification of the *Cryptosporidium* species/subtype and its corresponding sequence for each sample. </help> <citations> <citation type="bibtex"> @misc{githubCryptoGenotyper, author = {Yanta C, Bessonov K, Robinson G, Troell K, Guy R}, title = {CryptoGenotyper: a new bioinformatics tool to enhance Cryptosporidium identification}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/phac-nml/CryptoGenotyper} }</citation> </citations> </tool>