comparison dada2_makeSequenceTable.xml @ 5:ec4a183cc713 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

4:383501d6aeb0

    Rscript '$dada2_script'
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
@READ_FOO@

library(dada2, quietly=T)
#if $plot == "yes"
library(ggplot2, quietly=T)
#end if

samples <- list()
#for $s in $samples:
    #if $len($samples) == 1
    samples <- readRDS('$s')
    #else
    samples[["$s.element_identifier"]] <- readRDS('$s')
    #end if
#end for
## make sequence table
seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")


reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)

#if $plot == "yes"

bequiet <- dev.off()
#end if

## filter by seqlengths
#if $filter_cond.filter_select != "no"
    seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max)]
#end if

write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
    ]]></configfile>
    </configfiles>
    <inputs>
        <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
        <param argument="orderBy" type="select" label="Column order">
            <option value="abundance">abundance</option>
            <option value="nsamples">nsamples</option>
        </param>
        <conditional name="filter_cond">

        <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
            <filter>plot</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
            <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
        </test>
    </tests>
    <help><![CDATA[
Description

5:ec4a183cc713

    Rscript '$dada2_script'
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
@READ_FOO@
@WRITE_FOO@

library(dada2, quietly=T)
#if $plot == "yes"
library(ggplot2, quietly=T)
#end if

samples <- list()
#for $s in $samples:
    samples[["$s.element_identifier"]] <- readRDS('$s')
#end for

seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")

reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)

#if $plot == "yes"

bequiet <- dev.off()
#end if

## filter by seqlengths
#if $filter_cond.filter_select != "no"
    seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max), drop=F]
#end if
write.data( seqtab, '$stable', "dada2_sequencetable" )
    ]]></configfile>
    </configfiles>
    <inputs>
        <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
        <param argument="orderBy" type="select" label="Column order">
            <option value="abundance">abundance</option>
            <option value="nsamples">nsamples</option>
        </param>
        <conditional name="filter_cond">

        <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
            <filter>plot</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
            <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
            <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" />
        </test>
        <test expect_num_outputs="1">
            <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
            <param name="filter_cond|filter_select" value="minmax"/>
            <param name="filter_cond|min" value="200"/>
            <param name="filter_cond|max" value="300"/>
            <param name="plot" value="no" />
            <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
        </test>
    </tests>
    <help><![CDATA[
Description