<tool id="_dropletBarcodePlot" name="Droplet barcode rank plot" version="1.6.1+galaxy2" profile="18.01">
    <description>Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data</description>
    <requirements>
      <requirement type="package" version="0.0.1">scxa-plots</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        $__tool_directory__/dropletBarcodePlot.R --output-plot "${plot_file}" --output-thresholds "${thresholds_file}" --label "${label}" --density-bins "${density_bins}" --roryk-multiplier "${roryk_multiplier}"
#if $input.type == 'mtx_matrix'
--mtx-matrix ${input.mtx_matrix}
#if $input.cellsbyrow
--cells-by-row
#end if
#end if
#if $input.type == 'barcode_freqs'
--barcode-frequencies ${input.barcode_frequencies}
#end if
	    ]]></command>

    <inputs>
        <conditional name="input">
          <param name="type" type="boolean" truevalue='mtx_matrix' falsevalue='barcode_freqs' checked="true" label="Input MTX-format matrix?" help="Barcode frequencies will be calculated for you. The alternative is to provide barcode frequencies directly"/>
          <when value="mtx_matrix">
            <param name="mtx_matrix" type="data" format="mtx" label="Matrix-market format matrix file, with cells by column (overrides --barcode-frequencies if supplied)" />
            <param name="cellsbyrow" type="boolean" checked="false" label="For use with --mtx-matrix: force interpretation of matrix to assume cells are by row, rather than by column (default)"/>
          </when>
          <when value="barcode_freqs">
            <param name="barcode_frequencies" type="data" format="txt" label="A two-column tab-delimited file, with barcodes in the first column and frequencies in the second" />
          </when>
        </conditional>
        <param name="label" type="text" optional='true' value="" label="Label to place in plot title"/>
        <param name="density_bins" type="integer" value="50" label="Number of bins used in barcode count frequency distribution"/>
        <param name="roryk_multiplier" type="float" value="1.5" label="Above-baseline multiplier to calculate roryk threshold"/>
    </inputs>

    <outputs>
        <data name="plot_file" format="png" label="${tool.name} on ${on_string}: barcode rank plot"/>
        <data name="thresholds_file" format="txt" label="${tool.name} on ${on_string}: barcode thresholds"/>
    </outputs>

    <tests>
      <test>
        <conditional name='input'>
          <param name="type" value="barcode_freqs"/>
          <param name="barcode_frequencies" ftype="txt" value="raw_cb_frequency.txt"/>
        </conditional>
        <output name="plot_file" file="barcode_plot.png"/>
      </test>
    </tests>

    <help><![CDATA[
.. class:: infomark

**What it does**

Given a barcode freqeuncy table or an MTX-format matrix from which one can be calculated, produces a barcode rank plot to assess distinctness of droplets with cells over those without (a key mark of good-quality droplet single-cell RNA-seq data).

Thresholds are calculated and plotted, either with DropletUtils or by custom method discussed at https://github.com/COMBINE-lab/salmon/issues/362#issuecomment-490160480.

**Inputs**

    * two-column tab-delimted text file with barcode frequencies OR an MTX-format matrix file

-----

**Outputs**

    * PNG-format plot file.
]]></help>
<citations>
  <citation type="bibtex">
@misc{github-hinxton-single-cell,
author = {Jonathan Manning, EBI Gene Expression Team},
year = {2019},
title = {Hinxton Single Cell Anlysis Environment},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
  }</citation>
</citations>
</tool>