annotate blobtools_plot.xml @ 0:234b3e869b16 draft default tip

"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"

<tool id="blobtools_plot" name="Blobtools plot" version="1.1" >
    <description>Generate Blobtools plot</description>
    <xrefs>
        <xref type='bio.tools'>blobtools</xref>
    </xrefs>
    <macros>
	  <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" /> 
    <command><![CDATA[
	    @SET_TMP_DIR@ &&
	    cp $input_json input.json &&
	    blobtools plot
	    -i input.json 
	    -o output 

	    ]]></command>
    <inputs>
	    <param name="input_json" type="data" format="json" label="json File" help="Input BlobDB json file"/>
	    <section name="adv_options" title="Advance Options" expanded="False">
		<param argument="--notitle" type="boolean" truevalue="--notitle" falsevalue="" checked="false" label="Title" help="Do not add filename as title to plot"/>
		<param argument="--filelabel" type="boolean" truevalue="--filelabel" falsevalue="" checked="false" label="File Label" help="Label axis based on filenames"/>
                <param argument="--length" type="integer" value="100" label="Minimum Sequence Length" help="Minimum sequence length considered for plotting [default: 100]"/>
                <param argument="--cindex" type="boolean" truevalue="--cindex" falsevalue="" checked="false" label="Colour" help="Colour blobs by 'c index' [default: False]"/>
                <param argument="--nohit" type="boolean" truevalue="--nohit" falsevalue="" checked="false" label="Hide sequence" help="Hide sequences without taxonomic annotation [default: False]"/>
	        <param argument="--noscale" type="boolean" truevalue="--noscale" falsevalue="" checked="false" label="Scale sequence" help="Do no scale sequences by length [default: False]"/>
                <param argument="--legend" type="boolean" truevalue="--legend" falsevalue="" checked="false" label="Plot legend" help="Plot legend of bobplot in separate figure"/>
                <param argument="--multiplot" type="boolean" truevalue="--multiplot" falsevalue="" checked="false" label="Multi-plot" help="Print blobplot for each taxonomic separately"/>
                <param argument="--sort" type="text" value="span" label="Sort order" help="Sort order for plotting [default: span]"/>
                <param name="taxrule" type="select" display="radio" label="Taxonomy Rule" help="Taxonomy rule for computing taxonomy: default bestsum">
                      <option selected="true" value="bestsum">best sum</option>
                      <option value="bestsumorder">best sum order</option>
                </param>
                <param name="rank" type="select" display="radio" label="Taxonomic rank">
                          <option value="species">Species</option>
                          <option value="genus">Genus</option>
                          <option value="family">Family</option>
                          <option value="order">Order</option>
                          <option value="phylum" selected="true">Phylum</option>
                          <option value="superkingdom">Superkingdom</option>
                          <option value="all">All</option>
                </param>
                <param argument="--label" type="text" value="" label="Groups label" help="Relabel (taxonomic) groups, can be used several times."/>
	    </section>
    </inputs>
    <outputs>

	    <data name="coverage" format="png" from_work_dir="output*.blobplot.cov0.*" label="${tool.name} on ${on_string} : coverage"/>
	    <data name="read_coverage" format="png" from_work_dir="output*.read_cov.cov0.*" label="${tool.name} on ${on_string} : read coverage"/>
	    <data name="statistic" format="txt" from_work_dir="output*.stats.txt" label="${tool.name} on ${on_string} : statistics "/>
    </outputs>

    <tests>
	 <test>
	     <!-- #1 blobtools create -->
            <param name="input_json" value="test.blobDB.json" ftype="json"/>
	    <output name="coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.bam0.png" ftype="png"/>
	    <output name="read_coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.read_cov.bam0.png" ftype="png"/>
            <output name="statistic" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.stats.txt" ftype="txt"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**
	    
*To visualize, quality control and taxonomic partitioning of genome datasets. Blobtools plot is used to produce two coverage plot in png format and a statistic file.*
	    
**Input**
	    
- Blob file - a Blob json file. 

**Parameters**

- infile - BlobDB file (created with "blobtools create")
- lib - Plot only certain covlib(s). Separated by ","
- notitle - Do not add filename as title to plot
- filelabel - Label axis based on filenames
- plotgroups INT - Number of (taxonomic) groups to plot, remaining groups are placed in 'other' [default: 8]
- length INT - Minimum sequence length considered for plotting [default: 100]
- cindex - Colour blobs by 'c index' [default: False]
- nohit - Hide sequences without taxonomic annotation [default: False] 
- noscale - Do not scale sequences by length [default: False]
- legend - Plot legend of blobplot in separate figure
- multiplot - Multi-plot. Print blobplot for each (taxonomic) group separately
- cumulative - Print plot after addition of each (taxonomic) group
- sort <ORDER> - Sort order for plotting [default: span] 1) span  : plot with decreasing span 2) count : plot with decreasing count
- hist <HIST> - Data for histograms [default: span] 1) span  : span-weighted histograms 2) count : count histograms
- rank <RANK> - Taxonomic rank used for colouring of blobs [default: phylum] (Supported: species, genus, family, order,phylum, superkingdom)	
- taxrule <TAXRULE> - Taxrule which has been used for computing taxonomy (Supported: bestsum, bestsumorder) [default: bestsum]
- format FORMAT -  Figure format for plot (png, pdf, eps, jpeg,ps, svg, svgz, tiff) [default: png]
- label GROUPS - Relabel (taxonomic) groups, can be used several times. e.g. "A=Actinobacteria,Proteobacteria
- colours COLOURFILE - File containing colours for (taxonomic) groups. This allows having more than 9 colours.
- exclude GROUPS - Exclude these (taxonomic) groups (also works for 'other') e.g. "Actinobacteria,Proteobacteria,other"
- refcov <FILE> - File containing number of "total" and "mapped" reads per coverage file. (e.g.: bam0,900,100). If provided, info will be used in read coverage plot(s).
-catcolour <FILE> - Colour plot based on categories from FILE (format : "seq category").


**Command line Example:**

- blobtools plot -i example_blobDB.json -o output_file_preifix

**Output**

- Coverage PNG file
- Read Coverage PNG file
- Statistic file
 
.. class:: infomark
	    
**Contributor**

Galaxy Australia wrapped the Blobtools: the original software is available in this `Github repository <https://github.com/DRL/blobtools>`_.

**References**
 
     ]]></help>
     <citations>
        <citation type="doi">DOI: 10.12688/f1000research.12232.1</citation>
     </citations>
</tool>