comparison crosscontamination_barcode_filter.xml @ 2:e20001675838 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 82a0fd493f5866b3ef65019709ae5c865998f802

1:78341ccbad0a

<tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@">
    <description>for use in plate-based barcoded analyses</description>
    <macros>
        <token name="@VERSION@">0.2</token>
        <macro name="sanitize_batch">
            <sanitizer invalid_char="">
                <valid initial="string.digits">
                    <add value=","/>
                </valid>

    )
)
#end if
regex.extract = '$advanced.regex_extract'
regex.display = '$advanced.regex_display'
out.pdf = '$out_plots'
out.table = '$out_table'
]]>
        </configfile>
    </configfiles>

                        <expand macro="sanitize_batch" />
                    </param>
                </repeat>
            </when>
        </conditional>
        <section name="advanced" expanded="false" title="RegEx Parameters" >
            <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" >
                <expand macro="sanitize_regex" />
            </param>
            <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" >
                <expand macro="sanitize_regex" />
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" />
        <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" />

                </repeat>
            </conditional>
            <output name="out_plots" value="out.pdf" compare="sim_size" />
            <output name="out_table" value="out.table" />
        </test>
    </tests>
    <help><![CDATA[
Cross-contamination Filter Plot
###################################

For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured.

If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).

.. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png
   :scale: 50 %

2:e20001675838

<tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@">
    <description>for use in plate-based barcoded analyses</description>
    <macros>
        <token name="@VERSION@">0.3</token>
        <macro name="sanitize_batch">
            <sanitizer invalid_char="">
                <valid initial="string.digits">
                    <add value=","/>
                </valid>

    )
)
#end if
regex.extract = '$advanced.regex_extract'
regex.display = '$advanced.regex_display'
sort.cells = as.logical('$advanced.sort_sizes')
out.pdf = '$out_plots'
out.table = '$out_table'
]]>
        </configfile>
    </configfiles>

                        <expand macro="sanitize_batch" />
                    </param>
                </repeat>
            </when>
        </conditional>
        <section name="advanced" expanded="false" title="Advanced Parameters" >
            <param name="regex_extract" type="text" value=".*P(\\d)_B(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" >
                <expand macro="sanitize_regex" />
            </param>
            <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" >
                <expand macro="sanitize_regex" />
            </param>
            <param name="sort_sizes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Sort Cells by Library Size" />
        </section>
    </inputs>
    <outputs>
        <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" />
        <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" />

                </repeat>
            </conditional>
            <output name="out_plots" value="out.pdf" compare="sim_size" />
            <output name="out_table" value="out.table" />
        </test>
        <test><!-- 12 Batch test -->
            <param name="input_table" value="b12.matrix" />
            <param name="input_barcodes" value="celseq_barcodes.192.raw" />
            <conditional name="inbuilt_spec" >
                <param name="select_use" value="custom" />
                <repeat name="barcode_format" >
                    <param name="range_start" value="1"/>
                    <param name="range_end" value="96" />
                    <param name="batches" value="1,3,5,7,9,11" />
                </repeat>
                <repeat name="barcode_format" >
                    <param name="range_start" value="97"/>
                    <param name="range_end" value="192" />
                    <param name="batches" value="2,4,6,8,10,12" />
                </repeat>
                <repeat name="plate_format" >
                    <param name="plate" value="1" />
                    <param name="batches" value="1,2,3,4" />
                </repeat>
                <repeat name="plate_format" >
                    <param name="plate" value="2" />
                    <param name="batches" value="5,6,7,8" />
                </repeat>
                <repeat name="plate_format" >
                    <param name="plate" value="3" />
                    <param name="batches" value="9,10,11,12" />
                </repeat>
            </conditional>
            <output name="out_plots" value="b12.pdf" compare="sim_size" />
            <output name="out_table" value="b12.table" />
        </test>
    </tests>
    <help><![CDATA[
Cross-contamination Filter Plot
###################################

For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured.
*Note -- Do not reuse batch numbering across plates!*

If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter).

.. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png
   :scale: 50 %