annotate dada2_makeSequenceTable.xml @ 2:99c6929236fa draft

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

<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
    <description>construct a sequence table (analogous to OTU table)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
    Rscript '$dada2_script'
    ]]></command>
    <configfiles>
        <configfile name="dada2_script"><![CDATA[
@READ_FOO@
@WRITE_FOO@

library(dada2, quietly=T)
#if $plot
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 $plot
pdf( '$plot_output' )
ggplot(data=df, aes(x=length, y=count)) +
    geom_col() +
#if $filter_cond.filter_select != "no"
    geom_vline( xintercept=c($filter_cond.min-0.5, $filter_cond.max+0.5) ) +
#end if
    theme_bw()
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="Order ASVs by">
            <option value="abundance">abundance</option>
            <option value="nsamples">nsamples</option>
        </param>
        <conditional name="filter_cond">
            <param name="filter_select" type="select" label="Length filter method">
                <option value="no">No filter</option>
                <option value="minmax">Specify minimum and maximum sequence lengths</option>
            </param>
            <when value="no"/>
            <when value="minmax">
                <param name="min" type="integer" value="" label="Minimum sequence length"/>
                <param name="max" type="integer" value="" label="Maximum sequence length"/>
            </when>
        </conditional>
        <param name="plot" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="plot sequence length distribution" />
    </inputs>
    <outputs>
        <data name="stable" format="dada2_sequencetable" label="${tool.name} on ${on_string}"/>
        <data name="plot_output" format="pdf" label="${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_S188_L001.Rdata,mergePairs_F3D141_S207_L001.Rdata"/>
			<output name="stable" value="makeSequenceTable.tab" ftype="dada2_sequencetable" lines_diff="2"/>
            <output name="plot_output" value="makeSequenceTable.pdf" ftype="pdf" compare="sim_size" delta="3000" />
        </test>
        <test expect_num_outputs="1">
            <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0_S188_L001.Rdata,mergePairs_F3D141_S207_L001.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.tab" ftype="dada2_sequencetable" lines_diff="2" />
        </test>
    </tests>
    <help><![CDATA[
Description
...........

This function constructs a sequence table -- more precisely an amplicon sequence variant table (ASV) table -- a higher-resolution version of the OTU table produced by traditional methods.

The sequence table is a matrix with rows corresponding to (and named by) the samples, and columns corresponding to (and named by) the sequence variants.

Usage
.....

**Input**: The result of dada, or mergePairs.

**Output**: A data set of type dada2_sequencetable, i.e. a tabular with a row for each sample, and a column for each unique sequence across all the samples. The columns are named by the sequence.

Details
.......

Sequences that are much longer or shorter than expected may be the result of non-specific priming. You can remove non-target-length by applying a length filter. This is analogous to “cutting a band” in-silico to get amplicons of the targeted length.

@HELP_OVERVIEW@
    ]]></help>
    <expand macro="citations"/>
</tool>