Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
view data_manager/install_primer_scheme_bedfiles.xml @ 2:b3710e492ee4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
author | iuc |
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date | Mon, 22 Jun 2020 18:26:10 -0400 |
parents | cce5d9327cd6 |
children | a2953ef09fe1 |
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<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.11" tool_type="manage_data" profile="19.05"> <requirements> <requirement type="package" version="2.24.0">requests</requirement> </requirements> <!-- fetch all the primers in one go --> <command detect_errors="exit_code"> python '$__tool_directory__/install_primer_scheme_bedfiles.py' '${output_file}' #if $input.input_type == "ARTIC" --artic_primers '${input.primers}' #else --primer_file '${input.primer_input}' --primer_name '${input.primer_name}' --primer_description '${input.primer_description}' #end if </command> <inputs> <conditional name="input"> <param name="input_type" label="Choose the source for primer schemes" type="select"> <option value="ARTIC" selected="true">ARTIC SARS-CoV-2 Github page</option> <option value="history">History</option> </param> <when value="ARTIC"> <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option> <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option> <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option> </param> </when> <when value="history"> <param name="primer_input" label="Select history item" type="data" format="bed" /> <param name="primer_name" label="Name for this primer scheme" type="text" help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" /> <param name="primer_description" label="Description for primer scheme" type="text" /> </when> </conditional> </inputs> <outputs> <data name="output_file" format="data_manager_json"/> </outputs> <tests> <test> <param name="input_type" value="ARTIC" /> <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/> <output name="output_file"> <assert_contents> <has_text text="ARTIC"/> </assert_contents> </output> </test> <test> <param name="input_type" value="history" /> <param name="primer_input" ftype="bed" value="sample1.bed" /> <param name="primer_name" value="sample_primer" /> <param name="primer_description" value="sample primer scheme" /> <output name="output_file"> <assert_contents> <has_text text="sample_primer"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ Amplicon sequencing for viral pathogens using the `PrimalSeq and iVar`_ relies on identifying primer locations in a reference sequence using BED format files. This data manager populates a Galaxy tool data table, either from files provided via a history or via the ARTIC_ network Github repository. .. _PrimalSeq and iVar: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7 .. _ARTIC: https://artic.network/ ]]></help> <citations> <citation type="doi">10.1186/s13059-018-1618-7</citation> </citations> </tool>