Mercurial > repos > iuc > merqury

annotate merqury_plot_CN.xml @ 6:eb7b00ec347d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 9aec17d26f63629419228ef07e76e789e5244891
author iuc
date Sat, 13 Apr 2024 19:17:55 +0000
parents d7edbc9c3a07
children
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d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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1 <tool id="merquryplot" name="Merqury histogram plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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2 <description>evaluate the assembly quality</description>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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3 <macros>
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4 <import>macros.xml</import>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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5 </macros>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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6 <expand macro="bio_tools"/>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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7 <expand macro="requirements"/>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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8 <version_command>merqury --version</version_command>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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9 <command detect_errors="exit_code"><![CDATA[
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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10 mkdir -p output_files/ &&
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eb7b00ec347d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 9aec17d26f63629419228ef07e76e789e5244891
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11 export MERQURY="\$(dirname \$(which merqury.sh))/../share/merqury" &&
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d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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12 \$MERQURY/plot/plot_spectra_cn.R
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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13 -f '$input1'
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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14 -o output_files/merqury_plot
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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15 #if $z
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16 --zero-hist '$z'
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17 #end if
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18 #if $cutoff
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19 --cutoff '$cutoff'
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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20 #end if
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21 --xdim $xdim
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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22 --ydim $ydim
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23 #if $xmax>0
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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24 --xmax $xmax
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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25 #end if
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26 #if $ymax>0
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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27 --ymax $ymax
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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28 #end if
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29 --type $type
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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30 #if $output_selector=='pdf'
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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31 -p
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32 #end if
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33
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34 ]]> </command>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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35 <inputs>
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36 <param argument="-f" type="data" name="input1" format="tabular" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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37 <param argument="--xdim" type="integer" label="Width of plot" value="6" min="0" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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38 <param argument="--ydim" type="integer" label="Height of plot" value="5" min="0" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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39 <param argument="--xmax" type="float" label="Maximum limit for k-mer multiplicity (leave 0 for default)" value="0" min="0" help="default: (x where y=peak) * 2.1" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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40 <param argument="--ymax" type="float" label="Maximum limit for k-mer count (leave 0 for default)" value="0" min="0" help="default: (y where y=peak) * 1.1" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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41 <param argument="-z" type="data" label="Assembly only counts" format="tabular" help=".only.hist file " optional="true" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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42 <param argument="--cutoff" type="data" label="Solid k-mer cutoffs" format="txt" help="cutoff.txt file" optional="true" />
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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43 <param name="output_selector" type="select" label="Output format" argument="-p">
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44 <option value="png" selected="true">PNG</option>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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45 <option value="pdf">PDF</option>
d7edbc9c3a07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
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46 </param>
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47 <param argument="--type" type="select" label="Type of plot (default all)">
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48 <option value="all" selected="true">All</option>
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49 <option value="line">Line</option>
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50 <option value="fill">Fill</option>
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51 <option value="stack">Stack</option>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png plots">
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56 <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
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57 <filter>"png" in output_selector</filter>
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58 </collection>
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59 <collection name="pdf_files" type="list" label="${tool.name} on ${on_string}: pdf plots">
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60 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" format="pdf" directory="output_files"/>
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61 <filter>"pdf" in output_selector</filter>
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62 </collection>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
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66 <param name="input1" value="output_merqury.assembly_01.spectra-cn.tabular"/>
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67 <param name="xdim" value="6" />
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68 <param name="ydim" value="5" />
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69 <param name="xmax" value="0" />
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70 <param name="ymax" value="0" />
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71 <param name="z" value="output_merqury.assembly_01.only.tabular"/>
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72 <param name="type" value="all" />
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73 <param name="output_selector" value="png" />
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74 <output_collection name="png_files" type="list" count="3">
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75 <element name="merqury_plot.fl">
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76 <assert_contents>
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77 <has_size value="99000" delta="5000"/>
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78 </assert_contents>
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79 </element>
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80 <element name="merqury_plot.ln">
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81 <assert_contents>
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82 <has_size value="99000" delta="5000"/>
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83 </assert_contents>
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84 </element>
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85 <element name="merqury_plot.st">
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86 <assert_contents>
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87 <has_size value="124000" delta="20000"/>
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88 </assert_contents>
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89 </element>
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90 </output_collection>
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91 </test>
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92 </tests>
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93
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94 <help><![CDATA[
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95
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96 .. class:: infomark
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97
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98 **Purpose**
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99 Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be
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100 generated. Inputs : Histogram files generated by merqury.
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101
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102 ]]> </help>
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103 <expand macro="citations"/>
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104 </tool>
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105