view dada2_assignTaxonomyAddspecies.xml @ 0:60abca9ae15f draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty

<tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@DADA2_VERSION@">
    <description>Learn Error rates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
    Rscript '$dada2_script' \${GALAXY_SLOTS:-1}
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
@READ_FOO@

library(dada2, quietly=T)

args <- commandArgs(trailingOnly = TRUE)
nthreads <- as.integer(args[1])

seqs <- $read_data($seqs)

#if $reference_cond.reference_select == history
ref <- '$refFasta'
#else
ref <- $reference_cond.refFasta.fields.path
#end if

taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC,
            outputBootstraps = $outputBootstraps, multithread = nthreads)

#if $outputBootstraps
    boot <- taxa$boot
    taxa <- taxa$taxa
#end if


#if $addSpecies_cond.addSpecies_select == "TRUE"
    #if $addSpecies_cond.allowMultiple_cond.allowMultiple == "num"
    aM <- $addSpecies_cond.allowMultiple_cond.num
    #else
    aM <- $addSpecies_cond.allowMultiple_cond.allowMultiple
    #end if
    #if $addSpecies_cond.speciesreference_cond.reference_select == history
    ref <- '$addSpecies_cond.speciesreference_cond.speciesrefFasta'
    #else
    ref <- '$addSpecies_cond.speciesreference_cond.speciesrefFasta.fields.path'
    #end if
    taxa <- addSpecies(taxa, '$addSpecies_cond.speciesRefFasta', allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)
#end if

#if $outputBootstraps
    TODO output boot 
#end if

write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)
    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="seqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="sequences to be assigned" help=""/>
        <conditional name="reference_cond">
          <param name="reference_select" type="select" label="Select a reference dataset your history or use a built-in?">
            <option value="builtin">Use a built-in reference</option>
            <option value="history">Use reference data from the history</option>
          </param>
          <when value="builtin">
            <param name="refFasta" type="select" label="Select reference data set" help="If a reference data set of interest is not listed, contact the Galaxy administrators">
              <options from_data_table="dada2_taxonomy">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>
          <when value="history">
            <param name="refFasta" type="data" format="fasta,fasta.gz" label="Reference data set" />
          </when>
        </conditional>
        <param name="minBoot" type="integer" value="50" min="0" label="Minimum bootstrap confidence" help="for assigning a
taxonomic level"/>
        <param name="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
        <param name="outputBootstraps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Output bootstrap values"/>

        <conditional name="addSpecies_cond">
            <param name="addSpecies_select" type="select" label="Add genus-species binomials to the taxonomic table">
                <option value="FALSE">No</option>
                <option value="TRUE">Yes</option>
            </param>
            <when value="FALSE"/>
            <when value="TRUE">
                <conditional name="speciesreference_cond">
                  <param name="speciesreference_select" type="select" label="Select a reference dataset your history or use a built-in?">
                    <option value="builtin">Use a built-in reference</option>
                    <option value="history">Use reference data from the history</option>
                  </param>
                  <when value="builtin">
                    <param name="speciesrefFasta" type="select" label="Select reference data set" help="If a reference data set of interest is not listed, contact the Galaxy administrators">
                      <options from_data_table="dada2_species">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                      </options>
                    </param>
                  </when>
                  <when value="history">
                    <param name="speciesrefFasta" type="data" format="fasta,fasta.gz" label="Reference data set" />
                  </when>
                </conditional>
                <conditional name="allowMultiple_cond">
                    <param name="allowMultiple" type="select" label="reporting options">
                        <option value="FALSE">only unambiguous identifications</option>
                        <option value="TRUE">all exactly matched species</option>
                        <option value="num">specify the maximal number of reported exactly matched species</option>
                    </param>
                    <when value="FALSE"/>
                    <when value="TRUE"/>
                    <when value="num">
                        <param name="num" type="integer" value="" min="1" label="Number of matched species"/>
                    </when>
                </conditional>
                <param name="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
    </outputs>

    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
    <expand macro="citations"/>
</tool>