Mercurial > repos > iuc > poretools_yield_plot

comparison poretools_yield_plot.xml @ 1:b17593289ad0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
author iuc
date Sun, 19 Jan 2020 14:05:14 +0000
parents a8c8a7354ab7
children d4bbe0275728
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0:a8c8a7354ab7 1:b17593289ad0
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.0"> 2 <tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.1">
3 <description>of sequencing yield over time</description> 3 <description>of sequencing yield over time</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive">
9 <![CDATA[ 9 <![CDATA[
10 poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type 10 @MPLBACKEND@
11 $theme_bw 11 poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
12 #if $skip != '0': 12 $theme_bw
13 --skip $skip 13 #if $skip != '0':
14 #end if 14 --skip $skip
15 && mv plot.$extension '$output' 15 #end if
16 && mv plot.$extension '$output'
16 ]]> 17 ]]>
17 </command> 18 </command>
18 <inputs> 19 <inputs>
19 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> 20 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
20 <param name="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs"> 21 <param name="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs">
21 <option value="reads">Reads</option> 22 <option value="reads">Reads</option>
22 <option value="basepairs">Base pairs</option> 23 <option value="basepairs">Base pairs</option>
23 </param> 24 </param>
24 <param argument="--skip" type="integer" value="0" label="Plot only every nth point" help="Increases performance at the cost of resolution." /> 25 <param argument="--skip" type="integer" min="1" value="1" label="Plot only every nth point" help="Increases performance at the cost of resolution." />
25 <expand macro="plot_options" /> 26 <expand macro="plot_options" />
26 </inputs> 27 </inputs>
27 <outputs> 28 <outputs>
28 <expand macro="image_output" /> 29 <expand macro="image_output" />
29 </outputs> 30 </outputs>
30 <tests> 31 <tests>
31 <test> 32 <test>
32 <expand macro="test_input" /> 33 <expand macro="test_input" />
33 <param name="extension" value="png" /> 34 <param name="extension" value="png" />
34 <param name="plot_type" value="reads" /> 35 <param name="plot_type" value="reads" />
35 <output name="output" file="poretools-yield-plot-out1.png" ftype="png" lines_diff="301" /> 36 <output name="output" file="poretools-yield-plot-out1.png" ftype="png" compare="sim_size" />
36 </test> 37 </test>
37 <test> 38 <test>
38 <expand macro="test_input" /> 39 <expand macro="test_input" />
39 <param name="extension" value="svg" /> 40 <param name="extension" value="svg" />
40 <param name="plot_type" value="basepairs" /> 41 <param name="plot_type" value="basepairs" />
41 <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="40" /> 42 <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="50" />
42 </test> 43 </test>
43 </tests> 44 </tests>
44 <help> 45 <help>
45 Create a collector’s curve reflecting the sequencing yield over time. 46 Create a collector’s curve reflecting the sequencing yield over time.
46 </help> 47 </help>