Mercurial > repos > crusoe > khmer
changeset 29:e825c66d31de
filter-abund tests
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 16:22:35 -0400 |
| parents | c1f0790be1c4 |
| children | 36e447a9ac52 |
| files | filter-abund.xml |
| diffstat | 1 files changed, 34 insertions(+), 17 deletions(-) [+] |
line wrap: on
line diff
--- a/filter-abund.xml Sun Jun 29 16:07:06 2014 -0400 +++ b/filter-abund.xml Sun Jun 29 16:22:35 2014 -0400 @@ -15,6 +15,9 @@ <command> mkdir output; cd output; filter-abund.py +#if $cutoff != 2 + --cutoff=$cutoff +#fi $variable_coverage $countingtable_to_load #for input in $inputs @@ -31,6 +34,11 @@ falsevalue="" label="Variable coverage" help="Only trim when a sequence has high enough coverage (median abundance > 20)" /> + <param name="cutoff" + type="integer" + value="2" + label="cutoff" + help="Trim at k-mers below this abundance." /> <expand macro="input_counting_table_filename" /> </inputs> <outputs> @@ -41,23 +49,32 @@ <exit_code range="1:" level="fatal" /> </stdio> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> - <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory - <test> - <param name="input" value="input_test.tab" /> - <param name="int" value="10" /> - <output name="output" file="output_test.txt" /> - </test> --> - <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- - <test> - </test> ---> - </tests> - - <!-- [OPTIONAL] Help displayed in Galaxy --> + <tests> + <test> + <param name="inputs" value="test-abund-read-2.fa" /> + <param name="input_counting_table_filename" value="test-abund-read-2.ct" /> + <output name="output"> + <discover_dataset name="test-abund-read-2.fa.abundfilt"> + <assert_contents> + <has_text text="GGTTGACGGGGCTCAGGG" /> + </assert_contents> + </discover_dataset> + </output> + </test> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="input_counting_table_filename" value="test-abund-read-2.ct" /> + <param name="cutoff" value="1" /> + <output name="output"> + <discover_dataset name="test-abund-read-2.fa.abundfilt"> + <assert_contents> + <has_text text="GGTTGACGGGGCTCAGGG" /> + </assert_contents> + </discover_dataset> + </output> + </test> + </tests> + <!-- [OPTIONAL] Help displayed in Galaxy --> <!-- <help> </help>