Mercurial > repos > iuc > poretools_events
comparison poretools_events.xml @ 1:28d7819c312f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"
| author | iuc |
|---|---|
| date | Sun, 19 Jan 2020 09:10:59 -0500 |
| parents | 1d835c691480 |
| children | daf8518d243a |
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| 0:1d835c691480 | 1:28d7819c312f |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.0"> | 2 <tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1"> |
| 3 <description>from a set of sequencing reads</description> | 3 <description>from a set of sequencing 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" /> |
| 10 poretools events $precalled '$input' > '$output' | 10 poretools events $precalled '$input' > '$output' |
| 11 ]]> | 11 ]]> |
| 12 </command> | 12 </command> |
| 13 <inputs> | 13 <inputs> |
| 14 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> | 14 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> |
| 15 <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="--pre-basecalled" label="Report pre-basecalled events" /> | 15 <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" /> |
| 16 </inputs> | 16 </inputs> |
| 17 <outputs> | 17 <outputs> |
| 18 <data name="output" format="tabular" /> | 18 <data name="output" format="tabular" /> |
| 19 </outputs> | 19 </outputs> |
| 20 <tests> | 20 <tests> |
| 21 <test> | 21 <test> |
| 22 <expand macro="test_input" /> | 22 <expand macro="test_input" /> |
| 23 <param name="precalled" value="false" /> | 23 <param name="precalled" value="false" /> |
| 24 <output name="output" file="poretools-events-out1.tabular" ftype="tabular" /> | 24 <output name="output" ftype="tabular"> |
| 25 <assert_contents> | |
| 26 <has_n_lines n="2901"/> | |
| 27 <has_text text="template"/> | |
| 28 <has_text text="complement"/> | |
| 29 <not_has_text text="pre_basecalled"/> | |
| 30 </assert_contents> | |
| 31 </output> | |
| 25 </test> | 32 </test> |
| 26 <test> | 33 <test> |
| 27 <expand macro="test_input" /> | 34 <expand macro="test_input" /> |
| 28 <param name="precalled" value="true" /> | 35 <param name="precalled" value="true" /> |
| 29 <output name="output" file="poretools-events-out2.tabular" ftype="tabular" /> | 36 <output name="output" ftype="tabular"> |
| 37 <assert_contents> | |
| 38 <has_n_lines n="3083"/> | |
| 39 <not_has_text text="template"/> | |
| 40 <not_has_text text="complement"/> | |
| 41 <has_text text="pre_basecalled"/> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 30 </test> | 44 </test> |
| 31 </tests> | 45 </tests> |
| 32 <help> | 46 <help> |
| 33 Extract the raw nanopore events from each FAST5 file. | 47 Extract the raw nanopore events from each FAST5 file. |
| 34 </help> | 48 </help> |