Mercurial > repos > iuc > poretools_events
changeset 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 |
| files | macros.xml poretools_events.xml test-data/poretools-events-out1.tabular test-data/poretools-events-out2.tabular |
| diffstat | 4 files changed, 20 insertions(+), 6170 deletions(-) [+] |
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--- a/macros.xml Tue Dec 19 14:45:24 2017 -0500 +++ b/macros.xml Sun Jan 19 09:10:59 2020 -0500 @@ -47,4 +47,6 @@ <param name="min_length" argument="--min-length" type="integer" value="0" label="Minimum read length" /> <param name="max_length" argument="--max-length" type="integer" value="1000000000" label="Maximum read length" /> </xml> + <token name="@MPLBACKEND@"><![CDATA[export MPLBACKEND="agg" &&]]></token> + <token name="@profile@">18.09</token> </macros>
--- a/poretools_events.xml Tue Dec 19 14:45:24 2017 -0500 +++ b/poretools_events.xml Sun Jan 19 09:10:59 2020 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.0"> +<tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1"> <description>from a set of sequencing reads</description> <macros> <import>macros.xml</import> @@ -12,7 +12,7 @@ </command> <inputs> <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" /> - <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="--pre-basecalled" label="Report pre-basecalled events" /> + <param name="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" /> </inputs> <outputs> <data name="output" format="tabular" /> @@ -21,12 +21,26 @@ <test> <expand macro="test_input" /> <param name="precalled" value="false" /> - <output name="output" file="poretools-events-out1.tabular" ftype="tabular" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="2901"/> + <has_text text="template"/> + <has_text text="complement"/> + <not_has_text text="pre_basecalled"/> + </assert_contents> + </output> </test> <test> <expand macro="test_input" /> <param name="precalled" value="true" /> - <output name="output" file="poretools-events-out2.tabular" ftype="tabular" /> + <output name="output" ftype="tabular"> + <assert_contents> + <has_n_lines n="3083"/> + <not_has_text text="template"/> + <not_has_text text="complement"/> + <has_text text="pre_basecalled"/> + </assert_contents> + </output> </test> </tests> <help>
--- a/test-data/poretools-events-out1.tabular Tue Dec 19 14:45:24 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3083 +0,0 @@ -file strand mean start stdv length model_state model_level move p_model_state mp_model_state p_mp_model_state p_A p_C p_G p_T raw_index -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 52.3276716165 955054 5.19878084063 17 -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 45.2667833984 955071 1.3678974514 25 -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 55.5428768382 955096 4.1309184471 17 -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 81.4959472656 955113 5.98801696437 14 -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 89.1865418294 955127 0.657985513478 15 -.poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 pre_basecalled 91.2216268884 955142 0.745442845871 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