Mercurial > repos > iuc > merqury
comparison merqury_plot_CN.xml @ 5:d7edbc9c3a07 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 72d058b49b983b38e7565da1577d30fd2deec7d7
author | iuc |
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date | Fri, 16 Feb 2024 22:00:00 +0000 |
parents | |
children | eb7b00ec347d |
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4:09c589057ee8 | 5:d7edbc9c3a07 |
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1 <tool id="merquryplot" name="Merqury histogram plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> | |
2 <description>evaluate the assembly quality</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="bio_tools"/> | |
7 <expand macro="requirements"/> | |
8 <version_command>merqury --version</version_command> | |
9 | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 mkdir -p output_files/ && | |
12 \$MERQURY/plot/plot_spectra_cn.R | |
13 -f '$input1' | |
14 -o output_files/merqury_plot | |
15 #if $z | |
16 --zero-hist '$z' | |
17 #end if | |
18 #if $cutoff | |
19 --cutoff '$cutoff' | |
20 #end if | |
21 --xdim $xdim | |
22 --ydim $ydim | |
23 #if $xmax>0 | |
24 --xmax $xmax | |
25 #end if | |
26 #if $ymax>0 | |
27 --ymax $ymax | |
28 #end if | |
29 --type $type | |
30 #if $output_selector=='pdf' | |
31 -p | |
32 #end if | |
33 | |
34 ]]> </command> | |
35 <inputs> | |
36 <param argument="-f" type="data" name="input1" format="tabular" /> | |
37 <param argument="--xdim" type="integer" label="Width of plot" value="6" min="0" /> | |
38 <param argument="--ydim" type="integer" label="Height of plot" value="5" min="0" /> | |
39 <param argument="--xmax" type="float" label="Maximum limit for k-mer multiplicity (leave 0 for default)" value="0" min="0" help="default: (x where y=peak) * 2.1" /> | |
40 <param argument="--ymax" type="float" label="Maximum limit for k-mer count (leave 0 for default)" value="0" min="0" help="default: (y where y=peak) * 1.1" /> | |
41 <param argument="-z" type="data" label="Assembly only counts" format="tabular" help=".only.hist file " optional="true" /> | |
42 <param argument="--cutoff" type="data" label="Solid k-mer cutoffs" format="txt" help="cutoff.txt file" optional="true" /> | |
43 <param name="output_selector" type="select" label="Output format" argument="-p"> | |
44 <option value="png" selected="true">PNG</option> | |
45 <option value="pdf">PDF</option> | |
46 </param> | |
47 <param argument="--type" type="select" label="Type of plot (default all)"> | |
48 <option value="all" selected="true">All</option> | |
49 <option value="line">Line</option> | |
50 <option value="fill">Fill</option> | |
51 <option value="stack">Stack</option> | |
52 </param> | |
53 </inputs> | |
54 <outputs> | |
55 <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png plots"> | |
56 <discover_datasets pattern="(?P<name>.+)\.png" format="png" directory="output_files"/> | |
57 <filter>"png" in output_selector</filter> | |
58 </collection> | |
59 <collection name="pdf_files" type="list" label="${tool.name} on ${on_string}: pdf plots"> | |
60 <discover_datasets pattern="(?P<name>.+)\.pdf" format="pdf" directory="output_files"/> | |
61 <filter>"pdf" in output_selector</filter> | |
62 </collection> | |
63 </outputs> | |
64 <tests> | |
65 <test expect_num_outputs="1"> | |
66 <param name="input1" value="output_merqury.assembly_01.spectra-cn.tabular"/> | |
67 <param name="xdim" value="6" /> | |
68 <param name="ydim" value="5" /> | |
69 <param name="xmax" value="0" /> | |
70 <param name="ymax" value="0" /> | |
71 <param name="z" value="output_merqury.assembly_01.only.tabular"/> | |
72 <param name="type" value="all" /> | |
73 <param name="output_selector" value="png" /> | |
74 <output_collection name="png_files" type="list" count="3"> | |
75 <element name="merqury_plot.fl"> | |
76 <assert_contents> | |
77 <has_size value="99000" delta="5000"/> | |
78 </assert_contents> | |
79 </element> | |
80 <element name="merqury_plot.ln"> | |
81 <assert_contents> | |
82 <has_size value="99000" delta="5000"/> | |
83 </assert_contents> | |
84 </element> | |
85 <element name="merqury_plot.st"> | |
86 <assert_contents> | |
87 <has_size value="124000" delta="20000"/> | |
88 </assert_contents> | |
89 </element> | |
90 </output_collection> | |
91 </test> | |
92 </tests> | |
93 | |
94 <help><![CDATA[ | |
95 | |
96 .. class:: infomark | |
97 | |
98 **Purpose** | |
99 Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be | |
100 generated. Inputs : Histogram files generated by merqury. | |
101 | |
102 ]]> </help> | |
103 <expand macro="citations"/> | |
104 </tool> | |
105 |