comparison dada2_assignTaxonomyAddspecies.xml @ 2:1c9715cef808 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"

1:4d89978c6188

ref <- '$reference_cond.refFasta.fields.path'
tl <- '$reference_cond.refFasta.fields.taxlevels'
#end if
tl <- strsplit(tl, ",")[[1]]

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

#if $outputBootstraps

    #end if
    taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)
#end if
write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)

#if $outputBootstraps
    write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA)
#end if
    ]]></configfile>
    </configfiles>
    <inputs>

                    </when>
                </conditional>
                <param argument="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 ${on_string}"/>
        <data name="bootstraps" format="tabular" label="${tool.name} on ${on_string}: bootstraps">
            <filter>outputBootstraps</filter>
        </data>
    </outputs>
    <tests>
        <!-- test w default params -->
        <test expect_num_outputs="1">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
            <param name="reference_cond|reference_select" value="history"/>
            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
            <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
        </test>
         <!-- test w default params, bulit in reference -->
        <test expect_num_outputs="1">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
            <param name="reference_cond|reference_select" value="builtin"/>
            <param name="reference_cond|refFasta" value="test_buildid"/>
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
        </test>
        <!-- test w output bootstraps, minRC, note: sim_size for bootstraps output due to the probabilistics -->
        <test expect_num_outputs="2">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
            <param name="reference_cond|reference_select" value="history"/>
            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
            <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
            <param name="minBoot" value="42" />
            <param name="tryRC" value="TRUE" />
            <param name="outputBootstraps" value="TRUE" />
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
            <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
            <param name="addSpecies_cond|tryRC" value="TRUE" />
            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />
            <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Description
...........

2:1c9715cef808

ref <- '$reference_cond.refFasta.fields.path'
tl <- '$reference_cond.refFasta.fields.taxlevels'
#end if
tl <- strsplit(tl, ",")[[1]]

#if str($seed)
    set.seed($seed)
#end if

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

#if $outputBootstraps

    #end if
    taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)
#end if
write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)

#if $outputBootstraps == "TRUE"
    write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA)
#end if
    ]]></configfile>
    </configfiles>
    <inputs>

                    </when>
                </conditional>
                <param argument="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>
        <param name="seed" type="integer" value="" optional="true" label="Seed" help="Seed for the random number renerator. Set it in order to reproduce exactly the same results."/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
        <data name="bootstraps" format="tabular" label="${tool.name} on ${on_string}: bootstraps">
            <filter>outputBootstraps</filter>
        </data>
    </outputs>
    <tests>
        <!-- test w default params -->
        <test expect_num_outputs="1">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
            <param name="reference_cond|reference_select" value="history"/>
            <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa.gz"/>
            <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa.gz" />
            <param name="seed" value="42"/>
            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0"/>
        </test>
         <!-- test w default params, bulit in reference -->
        <test expect_num_outputs="2">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
            <param name="reference_cond|reference_select" value="builtin"/>
            <param name="reference_cond|refFasta" value="test_buildid"/>
            <param name="outputBootstraps" value="TRUE" />
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
            <param name="seed" value="42"/>
            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" delta="0" />
            <output name="bootstraps" value="assignTaxonomyAddspecies_boot.tab" ftype="tabular" compare="sim_size" delta="100" />
        </test>
        <!-- minRC, note: sim_size for bootstraps output due to the probabilistics -->
        <test expect_num_outputs="1">
            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo.tab"/>
            <param name="reference_cond|reference_select" value="history"/>
            <param name="reference_cond|refFasta" ftype="fasta.gz" value="reference.fa.gz"/>
            <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
            <param name="minBoot" value="42" />
            <param name="tryRC" value="TRUE" />
            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta.gz" value="reference_species.fa.gz" />
            <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
            <param name="addSpecies_cond|tryRC" value="TRUE" />
            <param name="seed" value="42"/>
            <output name="output" value="assignTaxonomyAddspecies.tab" ftype="tabular" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
Description
...........