Mercurial > repos > iuc > mykrobe_predict
view mykrobe_predict.xml @ 4:a2e3ad69ee23 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
author | iuc |
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date | Thu, 26 Aug 2021 20:38:36 +0000 |
parents | e8405163fb4e |
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<tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0" profile="@PROFILE@"> <description>Antibiotic resistance predictions</description> <macros> <import>macro.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import difflib #import re mykrobe predict --species '${select_species.species}' --panel '${select_species.panel}' #if $conf_percent_cutoff: --conf_percent_cutoff '${conf_percent_cutoff}' #end if #if $min_depth: --min_depth ${min_depth} #end if @shared_options@ -q -t "\${GALAXY_SLOTS:-1}" #if $data_type.type in ["single", "paired"]: #set read1 = $data_type.seq1 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) #if $data_type.type == "single": --sample '${read1_identifier}' --seq '${read1}' #else: #set read2 = $data_type.seq2 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks() #set match = $matches[0] #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size])) --sample '${identifier}' --seq '${read1}' '${read2}' #end if #elif $data_type.type == "collection": #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier)) --sample '${identifier}' --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}' #end if --format '${format}' > '$output']]> </command> <inputs> <expand macro="inputs"/> <conditional name="select_species"> <param name="species" type="select" label="Specify Species for AMR"> <option value="tb">Mycobacterium tuberculosis (tb)</option> <option value="staph">Staphylococcus aureus (staph)</option> <option value="sonnei">Shigella sonnei (sonnei)</option> </param> <when value="staph"> <param name="panel" type="select" label="Select panel for Staph only"> <option value="20170217">20170217</option> </param> </when> <when value="tb"> <param name="panel" type="select" label="Select panel for TB only"> <option value="202010">202010</option> <option value="201901">201901</option> <option value="bradley-2015">Bradely 2015</option> </param> </when> <when value="sonnei"> <param name="panel" type="select" label="Select panel for sonnei only"> <option value="20210201">20210201</option> <option value="20201012">20201012</option> </param> </when> </conditional> <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth" help=""/> <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff"> <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" /> </param> <expand macro="options"/> <param argument="--format" type="select" label="Select the prefered output format"> <option value="csv" >csv</option> <option value="json">json</option> </param> </inputs> <outputs> <data name="output" format="csv" label="prediction"> <change_format> <when input="format" value="json" format="json"/> </change_format> </data> </outputs> <tests> <test> <param name="type" value="single"/> <param name="seq1" ftype="fastq" value="reads.fastq"/> <param name="species" value="tb"/> <param name="panel" value="bradley-2015"/> <param name="format" value="json"/> <output name="output"> <assert_contents> <has_text_matching expression="susceptibility"/> </assert_contents> </output> </test> <test> <param name="type" value="single"/> <param name="seq1" ftype="fastq" value="reads.fastq"/> <param name="species" value="sonnei"/> <param name="panel" value="20201012"/> <param name="format" value="json"/> <output name="output"> <assert_contents> <has_text_matching expression="susceptibility"/> </assert_contents> </output> </test> <test> <param name="type" value="single"/> <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/> <param name="species" value="sonnei"/> <param name="panel" value="20201012"/> <param name="format" value="json"/> <output name="output"> <assert_contents> <has_text_matching expression="susceptibility"/> </assert_contents> </output> </test> </tests> <help> @ATTRIBUTION@ </help> <expand macro="citation" /> </tool>