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

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
author galaxy-australia
date Wed, 26 Oct 2022 06:54:04 +0000
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234b3e869b16 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
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1 <tool id="blobtools_plot" name="Blobtools plot" version="1.1" >
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2 <description>Generate Blobtools plot</description>
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3 <xrefs>
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4 <xref type='bio.tools'>blobtools</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 @SET_TMP_DIR@ &&
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14 cp $input_json input.json &&
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15 blobtools plot
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16 -i input.json
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17 -o output
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18
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19 ]]></command>
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20 <inputs>
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21 <param name="input_json" type="data" format="json" label="json File" help="Input BlobDB json file"/>
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22 <section name="adv_options" title="Advance Options" expanded="False">
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23 <param argument="--notitle" type="boolean" truevalue="--notitle" falsevalue="" checked="false" label="Title" help="Do not add filename as title to plot"/>
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24 <param argument="--filelabel" type="boolean" truevalue="--filelabel" falsevalue="" checked="false" label="File Label" help="Label axis based on filenames"/>
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25 <param argument="--length" type="integer" value="100" label="Minimum Sequence Length" help="Minimum sequence length considered for plotting [default: 100]"/>
234b3e869b16 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
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26 <param argument="--cindex" type="boolean" truevalue="--cindex" falsevalue="" checked="false" label="Colour" help="Colour blobs by 'c index' [default: False]"/>
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27 <param argument="--nohit" type="boolean" truevalue="--nohit" falsevalue="" checked="false" label="Hide sequence" help="Hide sequences without taxonomic annotation [default: False]"/>
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28 <param argument="--noscale" type="boolean" truevalue="--noscale" falsevalue="" checked="false" label="Scale sequence" help="Do no scale sequences by length [default: False]"/>
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29 <param argument="--legend" type="boolean" truevalue="--legend" falsevalue="" checked="false" label="Plot legend" help="Plot legend of bobplot in separate figure"/>
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30 <param argument="--multiplot" type="boolean" truevalue="--multiplot" falsevalue="" checked="false" label="Multi-plot" help="Print blobplot for each taxonomic separately"/>
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31 <param argument="--sort" type="text" value="span" label="Sort order" help="Sort order for plotting [default: span]"/>
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32 <param name="taxrule" type="select" display="radio" label="Taxonomy Rule" help="Taxonomy rule for computing taxonomy: default bestsum">
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33 <option selected="true" value="bestsum">best sum</option>
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34 <option value="bestsumorder">best sum order</option>
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35 </param>
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36 <param name="rank" type="select" display="radio" label="Taxonomic rank">
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37 <option value="species">Species</option>
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38 <option value="genus">Genus</option>
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39 <option value="family">Family</option>
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40 <option value="order">Order</option>
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41 <option value="phylum" selected="true">Phylum</option>
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42 <option value="superkingdom">Superkingdom</option>
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43 <option value="all">All</option>
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44 </param>
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45 <param argument="--label" type="text" value="" label="Groups label" help="Relabel (taxonomic) groups, can be used several times."/>
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46 </section>
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47 </inputs>
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48 <outputs>
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49
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50 <data name="coverage" format="png" from_work_dir="output*.blobplot.cov0.*" label="${tool.name} on ${on_string} : coverage"/>
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51 <data name="read_coverage" format="png" from_work_dir="output*.read_cov.cov0.*" label="${tool.name} on ${on_string} : read coverage"/>
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52 <data name="statistic" format="txt" from_work_dir="output*.stats.txt" label="${tool.name} on ${on_string} : statistics "/>
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53 </outputs>
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54
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55 <tests>
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56 <test>
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57 <!-- #1 blobtools create -->
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58 <param name="input_json" value="test.blobDB.json" ftype="json"/>
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59 <output name="coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.bam0.png" ftype="png"/>
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60 <output name="read_coverage" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.read_cov.bam0.png" ftype="png"/>
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61 <output name="statistic" file="test.blobDB.json.bestsum.phylum.p8.span.100.blobplot.stats.txt" ftype="txt"/>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65
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66 .. class:: infomark
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67
234b3e869b16 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
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68 **What it does**
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69
234b3e869b16 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
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70 *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.*
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71
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72 **Input**
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73
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74 - Blob file - a Blob json file.
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75
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76 **Parameters**
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77
234b3e869b16 "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/blobtools commit 89d41433582a6470135c026aad07b714eb3145d4"
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78 - infile - BlobDB file (created with "blobtools create")
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79 - lib - Plot only certain covlib(s). Separated by ","
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80 - notitle - Do not add filename as title to plot
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81 - filelabel - Label axis based on filenames
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82 - plotgroups INT - Number of (taxonomic) groups to plot, remaining groups are placed in 'other' [default: 8]
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83 - length INT - Minimum sequence length considered for plotting [default: 100]
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84 - cindex - Colour blobs by 'c index' [default: False]
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85 - nohit - Hide sequences without taxonomic annotation [default: False]
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86 - noscale - Do not scale sequences by length [default: False]
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87 - legend - Plot legend of blobplot in separate figure
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88 - multiplot - Multi-plot. Print blobplot for each (taxonomic) group separately
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89 - cumulative - Print plot after addition of each (taxonomic) group
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90 - sort <ORDER> - Sort order for plotting [default: span] 1) span : plot with decreasing span 2) count : plot with decreasing count
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91 - hist <HIST> - Data for histograms [default: span] 1) span : span-weighted histograms 2) count : count histograms
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92 - rank <RANK> - Taxonomic rank used for colouring of blobs [default: phylum] (Supported: species, genus, family, order,phylum, superkingdom)
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93 - taxrule <TAXRULE> - Taxrule which has been used for computing taxonomy (Supported: bestsum, bestsumorder) [default: bestsum]
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94 - format FORMAT - Figure format for plot (png, pdf, eps, jpeg,ps, svg, svgz, tiff) [default: png]
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95 - label GROUPS - Relabel (taxonomic) groups, can be used several times. e.g. "A=Actinobacteria,Proteobacteria
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96 - colours COLOURFILE - File containing colours for (taxonomic) groups. This allows having more than 9 colours.
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97 - exclude GROUPS - Exclude these (taxonomic) groups (also works for 'other') e.g. "Actinobacteria,Proteobacteria,other"
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98 - 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).
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99 -catcolour <FILE> - Colour plot based on categories from FILE (format : "seq category").
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100
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101
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102 **Command line Example:**
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103
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104 - blobtools plot -i example_blobDB.json -o output_file_preifix
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105
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106 **Output**
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107
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108 - Coverage PNG file
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109 - Read Coverage PNG file
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110 - Statistic file
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111
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112 .. class:: infomark
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113
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114 **Contributor**
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115
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116 Galaxy Australia wrapped the Blobtools: the original software is available in this `Github repository <https://github.com/DRL/blobtools>`_.
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117
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118 **References**
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119
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120 ]]></help>
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121 <citations>
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122 <citation type="doi">DOI: 10.12688/f1000research.12232.1</citation>
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123 </citations>
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124 </tool>