comparison nanoplot.xml @ 7:7b379e98b9a9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 15a00502ecd67b4908f392660c12988f972b6eab

6:0f1c34698076

<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="20.05">
    <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
    <macros>
        <token name="@TOOL_VERSION@">1.41.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
    </requirements>
    <stdio>
        <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem" />
    </stdio>
    <version_command>NanoPlot --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## set TMPDIR if not already set by admin
## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};

#end if

NanoPlot
    --threads \${GALAXY_SLOTS:-4}
    --tsv_stats
    --$mode.reads.type ${' '.join($reads_temp)}
    #if $filter.maxlength
        --maxlength $filter.maxlength
    #end if
    #if $filter.minlength

                        <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
                    </when>
                </conditional>
            </when>
        </conditional>
        <section
            name="filter"
            title="Options for filtering or transforming input prior to plotting"
            expanded="false">
            <param
                type="integer"
                argument="--maxlength"
                optional="true"
                label="Drop reads longer than length specified."/>
            <param
                type="integer"
                argument="--minlength"
                optional="true"
                label="Drop reads shorter than length specified."/>
            <param
                type="boolean"
                argument="--drop_outliers"
                truevalue="--drop_outliers"
                falsevalue=""
                label="Drop outlier reads with extreme long length."/>
            <param
                type="integer"
                argument="--downsample"
                optional="true"
                label="Reduce dataset to N reads by random sampling."/>
            <param
                type="boolean"
                argument="--loglength"
                truevalue="--loglength"
                falsevalue=""
                label="Logarithmic scaling of lengths in plots."/>
            <param
                type="boolean"
                argument="--percentqual"
                truevalue="--percentqual"
                falsevalue=""
                label="Use qualities as theoretical percent identities."/>
            <param
                type="boolean"
                argument="--alength"
                truevalue="--alength"
                falsevalue=""
                label="Use aligned read lengths rather than sequenced length (bam mode)."/>
            <param
                type="integer"
                argument="--minqual"
                optional="true"
                label="Drop reads with an average quality lower than specified."/>
            <param
                type="integer"
                argument="--runtime_until"
                optional="true"
                label="Only take the N first hours of a run"/>
            <param
                type="select"
                argument="--readtype"
                optional="true"
                label="Which read type to extract information about from summary.">
                <option value="1D">1D</option>
                <option value="2D">2D</option>
                <option value="1D2">1D2</option>
            </param>
            <param
                type="boolean"
                argument="--barcoded"
                truevalue="--barcoded"
                falsevalue=""
                label="Use if you want to split the summary file by barcode."/>
            <param
                type="boolean"
                argument="--no_supplementary"
                truevalue="--no_supplementary"
                falsevalue=""
                label="Use if you want to remove supplementary alignments"/>
        </section>
        <section
            name="customization"
            title="Options for customizing the plots created"
            expanded="false">
            <param
                type="select"
                argument="--color"
                optional="true"
                label="Specify a color for the plots.">
                <option value="aliceblue">aliceblue</option>
                <option value="antiquewhite">antiquewhite</option>
                <option value="aqua">aqua</option>
                <option value="aquamarine">aquamarine</option>
                <option value="azure">azure</option>

                <option value="whitesmoke">whitesmoke</option>
                <option value="white">white</option>
                <option value="yellowgreen">yellowgreen</option>
                <option value="yellow">yellow</option>
            </param>
            <param
                type="select"
                argument="--plots"
                optional="true"
                multiple="true"
                display="checkboxes"
                label="Specify the bivariate format of the plots.">
                <option value="kde">kernel density estimation (kde)</option>
                <option value="dot">dots (dot)</option>
            </param>
            <param
                type="boolean"
                argument="--N50"
                truevalue="--N50"
                falsevalue=""
                label="Show the N50 mark in the read length histogram."/>
        </section>
    </inputs>
    <outputs>
        <data name="output_html" format="html" from_work_dir="NanoPlot-report.html"  label="${tool.name} on ${on_string}: HTML report"/>
        <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
        <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering" />
        <data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
        <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/>
    </outputs>
    <tests>
        <test>
            <conditional name="mode">
                <param name="choice" value="batch"/>

                    <has_text text="mean_qual"/>
                </assert_contents>
            </output>
            <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
            <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
            <output name="read_length" ftype="png" file="HistogramReadlength.png" compare="sim_size">
            </output>
            <output name="log_read_length" ftype="png">
                <assert_contents>
                    <has_text text="PNG"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="mode">
                <param name="choice" value="combined"/>
                <conditional name="reads">

                <param name="color" value="yellow"/>
            </section>
            <output name="output_html" ftype="html">
                <assert_contents>
                    <has_text text="html"/>
                    <has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->
                </assert_contents>
            </output>
            <output name="read_length" ftype="png">
                <assert_contents>
                    <has_text text="PNG"/>
                </assert_contents>
            </output>
        </test>
        <test><!-- test with multiple input files -->
             <conditional name="mode">
                <param name="choice" value="combined"/>
                <conditional name="reads">
                    <param name="type" value="fasta"/>
                    <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />
                </conditional>
            </conditional>
            <output name="output_html" ftype="html">
                <assert_contents>
                    <has_text text="html"/>
                    <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
                    <has_text text="&lt;td&gt;9&lt;/td&gt;"/> <!--check both files were used 4+5 reads -->
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

7:7b379e98b9a9

<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0" profile="22.05">
    <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>
    <macros>
        <token name="@TOOL_VERSION@">1.42.0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">nanoplot</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>
    </requirements>
    <!--stdio>
        Not needed anymore, because we do not generate the static PNGs anymore.
        I will leave this in, in the case we activate the PNGs at some point again.
        <regex match="kaleido problem" source="stderr" level="fatal" description="No static plots are saved due to some kaleido problem"/>
    </stdio-->
    <version_command>NanoPlot --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
## set TMPDIR if not already set by admin
## otherwise kalleido fails with `Less than 64MB of free space in temporary directory for shared memory files: 0`
## export TMPDIR=\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR};

#end if

NanoPlot
    --threads \${GALAXY_SLOTS:-4}
    --tsv_stats
    --no_static
    --$mode.reads.type ${' '.join($reads_temp)}
    #if $filter.maxlength
        --maxlength $filter.maxlength
    #end if
    #if $filter.minlength

                        <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>
                    </when>
                </conditional>
            </when>
        </conditional>
        <section name="filter" title="Options for filtering or transforming input prior to plotting" expanded="false">
            <param argument="--maxlength" type="integer" optional="true" label="Drop reads longer than length specified."/>
            <param argument="--minlength" type="integer" optional="true" label="Drop reads shorter than length specified."/>
            <param argument="--drop_outliers" type="boolean" truevalue="--drop_outliers" falsevalue="" label="Drop outlier reads with extreme long length."/>
            <param argument="--downsample" type="integer" optional="true" label="Reduce dataset to N reads by random sampling."/>
            <param argument="--loglength" type="boolean" truevalue="--loglength" falsevalue="" label="Logarithmic scaling of lengths in plots."/>
            <param argument="--percentqual" type="boolean" truevalue="--percentqual" falsevalue="" label="Use qualities as theoretical percent identities."/>
            <param argument="--alength" type="boolean" truevalue="--alength" falsevalue="" label="Use aligned read lengths rather than sequenced length (bam mode)."/>
            <param argument="--minqual" type="integer" optional="true" label="Drop reads with an average quality lower than specified."/>
            <param argument="--runtime_until" type="integer" optional="true" label="Only take the N first hours of a run"/>
            <param argument="--readtype" type="select" optional="true" label="Which read type to extract information about from summary.">
                <option value="1D">1D</option>
                <option value="2D">2D</option>
                <option value="1D2">1D2</option>
            </param>
            <param argument="--barcoded" type="boolean" truevalue="--barcoded" falsevalue="" label="Use if you want to split the summary file by barcode."/>
            <param argument="--no_supplementary" type="boolean" truevalue="--no_supplementary" falsevalue="" label="Use if you want to remove supplementary alignments"/>
        </section>
        <section name="customization" title="Options for customizing the plots created" expanded="false">
            <param type="select" argument="--color" optional="true" label="Specify a color for the plots.">
                <option value="aliceblue">aliceblue</option>
                <option value="antiquewhite">antiquewhite</option>
                <option value="aqua">aqua</option>
                <option value="aquamarine">aquamarine</option>
                <option value="azure">azure</option>

                <option value="whitesmoke">whitesmoke</option>
                <option value="white">white</option>
                <option value="yellowgreen">yellowgreen</option>
                <option value="yellow">yellow</option>
            </param>
            <param type="select" argument="--plots" optional="true" multiple="true" display="checkboxes" label="Specify the bivariate format of the plots.">
                <option value="kde">kernel density estimation (kde)</option>
                <option value="dot">dots (dot)</option>
            </param>
            <param type="boolean" argument="--N50" truevalue="--N50" falsevalue="" label="Show the N50 mark in the read length histogram."/>
        </section>
    </inputs>
    <outputs>
        <data name="output_html" format="html" from_work_dir="NanoPlot-report.html" label="${tool.name} on ${on_string}: HTML report"/>
        <data name="nanostats" format="tabular" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: NanoStats"/>
        <data name="nanostats_post_filtering" format="tabular" from_work_dir="NanoStats_post_filtering.txt" label="${tool.name} on ${on_string}: NanoStats post filtering"/>
        <!-- https://github.com/wdecoster/NanoPlot/issues/352 generating PNGs can take much much longer to process. Not sure if this output is relevant at all -->
        <!--data name="read_length" format="png" from_work_dir="Non_weightedHistogramReadlength.png" label="${tool.name} on ${on_string}: Histogram Read Length"/>
        <data name="log_read_length" format="png" from_work_dir="Non_weightedLogTransformed_HistogramReadlength.png" label="${tool.name} on ${on_string}: Log Transformed Histogram Read Length"/-->
    </outputs>
    <tests>
        <test>
            <conditional name="mode">
                <param name="choice" value="batch"/>

                    <has_text text="mean_qual"/>
                </assert_contents>
            </output>
            <output name="nanostats" file="NanoStats.txt" ftype="tabular"/>
            <output name="nanostats_post_filtering" file="NanoStats_post_filtering.txt" ftype="tabular"/>
        </test>
        <test>
            <conditional name="mode">
                <param name="choice" value="combined"/>
                <conditional name="reads">

                <param name="color" value="yellow"/>
            </section>
            <output name="output_html" ftype="html">
                <assert_contents>
                    <has_text text="html"/>
                    <has_text text="Aligned read length vs Percent identity plot using dots"/>
                    <!-- bam report specific -->
                </assert_contents>
            </output>
        </test>
        <test>
            <!-- test with multiple input files -->
            <conditional name="mode">
                <param name="choice" value="combined"/>
                <conditional name="reads">
                    <param name="type" value="fasta"/>
                    <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta"/>
                </conditional>
            </conditional>
            <output name="output_html" ftype="html">
                <assert_contents>
                    <has_text text="html"/>
                    <not_has_text text="Aligned read length vs Percent identity plot using dots"/>
                    <has_text text="&lt;td&gt;9&lt;/td&gt;"/>
                    <!--check both files were used 4+5 reads -->
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>