comparison mykrobe_predict.xml @ 1:60ffb465aa4d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449

0:33463c79e697

<tool id="mykrobe_predict" name="mkyrobe predict" version="0.5.6" >
  <description>Antibiotic resistance predictions</description>
  <macros>
    <import>macro.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
<![CDATA[
         @select_inputs@

         mykrobe predict 
         '$name'
         $select_species.species


        #if $select_species.species =='tb':
          --panel $select_species.panel
        #end if



        #if $kmer:
          --kmer $kmer
        #end if

        #if $min_variant_conf:
          --min_variant_conf $min_variant_conf
        #end if


        #if $expected_depth:
          --expected_depth $expected_depth
        #end if


        #if $min_gene_conf:
          --min_gene_conf $min_gene_conf
        #end if



        #if $min_gene_percent_covg_threshold:
          --min_gene_percent_covg_threshold $min_gene_percent_covg_threshold
        #end if


        #if $min_depth:
          --min_depth $min_depth
        #end if


        #if $expected_error_rate:
          --expected_error_rate $expected_error_rate
        #end if

        $report_all_calls

        $ont
        -q
        -t "\${GALAXY_SLOTS:-1}"

        -1
        #if $type == 'fastq':
          *.fastq
        #else
          *.bam
        #end if
         > $json
]]>
  </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>
      </param>
      <when value="staph"/>
      <when value="tb">
        <param name="panel" type="select" label="Select panel for TB only">
          <option value="bradley-2015">Bradely 2015</option>
          <option value="walker-2015">Walker 2015</option>            
        </param>
      </when>
    </conditional>      
    <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
    <param name="expected_error_rate" argument="--expected_error_rate" optional="True" type="float" label="Expected Error Rate"  help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
    <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth"  help=""/>
    <param name="min_depth" argument="--min_depth" optional="True" type="integer" min="0" label="Minimum Depth"  help=""/>
    <param name="report_all_calls" argument="--report_all_calls"  type="boolean" truevalue="--report_all_calls" falsevalue="" label="report all calls"  help=""/>
    <param name="ont" argument="--ont"  type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
    <param name="min_variant_conf" argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>      
    <param name="min_gene_conf" argument="--min_gene_conf" optional="True" type="integer" min="0" label="minimum genotype confidence for gene genotyping"  help=""/>
    <param name="min_gene_percent_covg_threshold" argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum Gene predict coverage"  help="all genes alleles found above this percent coverage will be reported (default 100 (only best allelesreported))"/>      
  </inputs>

  <outputs>
    <data name="json" format="json" label="JSON prediction"/>
  </outputs>
  <tests>
    <test>
      <param name="type" value="single"/>
      <param name="fastq_input1" value="reads.fastq"/>
      <param name="species" value="tb"/>
      <param name="panel" value="bradley-2015"/>
      <output name="json">
        <assert_contents>
          <has_text_matching expression="variant_calls"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>

1:60ffb465aa4d

<tool id="mykrobe_predict" name="mkyrobe predict" version="0.6.1">
  <description>Antibiotic resistance predictions</description>
  <macros>
    <import>macro.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="exit_code">
<![CDATA[
        @select_inputs@

        mykrobe predict 
        '${name}'
        ${select_species.species}

        #if $select_species.panel == 'custom':
          #if $adv.custom_probe:
            --custom_probe_set_path '${adv.custom_probe}'
          #end if
          #if $adv.custom_variant_to_resistance:
            --custom_variant_to_resistance_json '${adv.custom_variant_to_resistance}'
          #end if
        #elif $select_species.panel:
          --panel '${select_species.panel}'
        #end if

        #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}"

        -1
        #if $type == 'fastq':
          *.fastq
        #else
          *.bam
        #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>
      </param>
      <when value="staph">
        <param name="panel" type="select" optional="true" label="Select panel for Staph only">
          <option value="custom">Custom</option>
        </param>
      </when>
      <when value="tb">
        <param name="panel" type="select" label="Select panel for TB only">
          <option value="201901">201901</option>
          <option value="bradley-2015">Bradely 2015</option>
          <option value="walker-2015">Walker 2015</option>
          <option value="custom">Custom</option>
        </param>
      </when>
    </conditional>
    <section name="adv" title="Custom Panel" expanded="false">
      <param name="custom_probe" type="data" format="fasta" label="Custom Probe" optional="True" help="Don't include filtered genotypes"/>
      <param name="custom_variant_to_resistance" type="data" format="json" label="Custom Variant to Resistance" optional="True" help="JSON file with key,value pairs of variant names and induced drug resistance."/>
    </section>
    <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="fastq_input1" 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>
  </tests>
  <help>