Mercurial > repos > iuc > bracken
changeset 8:1d4bd12f01cf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2d68ebc8d29e6046811970c6ef04f683e9916857
| author | iuc |
|---|---|
| date | Thu, 18 Jan 2024 15:38:05 +0000 |
| parents | 978ae4147c29 |
| children | 0c7b6eb7e752 |
| files | est-abundance.xml macros.xml test-data/NC_003198.1_simulated_bracken_report_S1.txt test-data/NC_003198.1_simulated_bracken_report_S2.txt test-data/test2.log |
| diffstat | 5 files changed, 25 insertions(+), 5 deletions(-) [+] |
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--- a/est-abundance.xml Mon May 22 19:24:46 2023 +0000 +++ b/est-abundance.xml Thu Jan 18 15:38:05 2024 +0000 @@ -33,6 +33,8 @@ </options> </param> <param name="level" type="select" label="Level" help="Level to push all reads to"> + <option value="S2">Subspecies 2</option> + <option value="S1">Subspecies 1</option> <option value="S" selected="true">Species</option> <option value="G">Genus</option> <option value="F">Family</option> @@ -74,6 +76,20 @@ <output name="kraken_report" file="NC_011750.1_simulated_kraken_style_bracken_report.txt" ftype="tabular"/> <output name="logfile" file="test2.log" lines_diff="8"/> </test> + <test expect_num_outputs="1"> + <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> + <param name="level" value="S1"/> + <param name="kmer_distr" value="test_entry"/> + <param name="logfile_output" value="False"/> + <output name="report" file="NC_003198.1_simulated_bracken_report_S1.txt" ftype="tabular"/> + </test> + <test expect_num_outputs="1"> + <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/> + <param name="level" value="S2"/> + <param name="kmer_distr" value="test_entry"/> + <param name="logfile_output" value="False"/> + <output name="report" file="NC_003198.1_simulated_bracken_report_S2.txt" ftype="tabular"/> + </test> </tests> <help> <![CDATA[
--- a/macros.xml Mon May 22 19:24:46 2023 +0000 +++ b/macros.xml Thu Jan 18 15:38:05 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.8</token> + <token name="@TOOL_VERSION@">2.9</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <xml name="requirements">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_bracken_report_S1.txt Thu Jan 18 15:38:05 2024 +0000 @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Salmonella enterica subsp. enterica 59201 S1 40 2 42 1.00000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_003198.1_simulated_bracken_report_S2.txt Thu Jan 18 15:38:05 2024 +0000 @@ -0,0 +1,2 @@ +name taxonomy_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads +Salmonella enterica subsp. enterica serovar Typhi 90370 S2 40 2 42 1.00000
--- a/test-data/test2.log Mon May 22 19:24:46 2023 +0000 +++ b/test-data/test2.log Thu Jan 18 15:38:05 2024 +0000 @@ -1,5 +1,5 @@ -PROGRAM START TIME: 08-05-2022 14:41:48 -BRACKEN SUMMARY (Kraken report: /tmp/tmpy56dgetr/files/f/5/4/dataset_f5412c50-3888-4466-b041-32814cdda47c.dat) +PROGRAM START TIME: 01-18-2024 14:06:58 +BRACKEN SUMMARY (Kraken report: /tmp/tmp49rzn0wx/files/f/a/a/dataset_faa2d0a2-78f4-4cc2-b304-c8202c4ffb77.dat) >>> Threshold: 10 >>> Number of species in sample: 1 >> Number of species with reads > threshold: 1 @@ -10,5 +10,5 @@ >> Reads distributed: 1 >> Reads not distributed (eg. no species above threshold): 0 >> Unclassified reads: 2 -BRACKEN OUTPUT PRODUCED: /tmp/tmpy56dgetr/job_working_directory/000/4/outputs/galaxy_dataset_e099cc44-07e6-4507-b11f-137722113078.dat -PROGRAM END TIME: 08-05-2022 14:41:48 +BRACKEN OUTPUT PRODUCED: /tmp/tmp49rzn0wx/job_working_directory/000/4/outputs/galaxy_dataset_27bf8d97-38f4-489a-a61b-6b567bbc8761.dat +PROGRAM END TIME: 01-18-2024 14:06:58