Mercurial > repos > iuc > poretools_occupancy

comparison poretools_occupancy.xml @ 1:338d15b8d6fb 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 09:09:55 -0500
parents 336791b5665f
children 0433aad600e9
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0:336791b5665f 1:338d15b8d6fb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="poretools_occupancy" name="Plot performance" version="@VERSION@.0"> 2 <tool id="poretools_occupancy" name="Plot performance" version="@VERSION@.1">
3 <description>per cell in nanopore reads</description> 3 <description>per cell in nanopore reads</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 occupancy 10 @MPLBACKEND@
11 '$input' 11 poretools occupancy
12 --saveas occupancy.$extension 12 '$input'
13 --plot-type $plot_type 13 --saveas occupancy.$extension
14 && 14 --plot-type $plot_type
15 mv occupancy.$extension '$output' 15 &&
16 mv occupancy.$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="extension" type="select" label="File format for histogram"> 21 <param name="extension" type="select" label="File format for histogram">
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <expand macro="test_input" /> 36 <expand macro="test_input" />
36 <param name="extension" value="png" /> 37 <param name="extension" value="png" />
37 <param name="plot_type" value="read_count" /> 38 <param name="plot_type" value="read_count" />
38 <output name="output" file="poretools-occupancy-out1.png" ftype="png" lines_diff="420" /> 39 <output name="output" file="poretools-occupancy-out1.png" ftype="png" compare="sim_size" />
39 </test> 40 </test>
40 <test> 41 <test>
41 <expand macro="test_input" /> 42 <expand macro="test_input" />
42 <param name="extension" value="pdf" /> 43 <param name="extension" value="pdf" />
43 <param name="plot_type" value="total_bp" /> 44 <param name="plot_type" value="total_bp" />
44 <output name="output" file="poretools-occupancy-out1.pdf" ftype="pdf" lines_diff="36" /> 45 <output name="output" file="poretools-occupancy-out1.pdf" ftype="pdf" lines_diff="384" />
45 </test> 46 </test>
46 </tests> 47 </tests>
47 <help> 48 <help>
48 Plot the throughput performance of each pore on the flowcell during a given sequencing run. 49 Plot the throughput performance of each pore on the flowcell during a given sequencing run.
49 </help> 50 </help>