Mercurial > repos > iuc > poretools_occupancy
comparison poretools_occupancy.xml @ 1:338d15b8d6fb draft default tip
"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 |
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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> |