Mercurial > repos > crusoe > khmer
changeset 13:3d81c3793820
first test
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 10:28:09 -0400 |
| parents | 760990dd7983 |
| children | d1403ee80c1e |
| files | abundance-dist-single.xml filter-abund.xml macros.xml test-data/test-abund-read-2.fa |
| diffstat | 4 files changed, 42 insertions(+), 27 deletions(-) [+] |
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--- a/abundance-dist-single.xml Sun Jun 29 09:50:29 2014 -0400 +++ b/abundance-dist-single.xml Sun Jun 29 10:28:09 2014 -0400 @@ -34,6 +34,18 @@ type="boolean" label="Save the k-mer counting table(s) in a file" help="" /> + <param name="no_zero" + type="boolean" + truevalue="" + falsevalue="--no_zero" + checked="true" + help="Output zero count bins" /> + <param name="no_bigcount" + type="boolean" + truevalue="" + falsevalue="--no_bigcount" + checked="true" + help="Count k-mers past 255" /> <expand macro="tableinputs" /> </inputs> <outputs> @@ -45,19 +57,21 @@ 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> ---> + <test> + <param name="input_sequence_filename" value="test-abund-read-2.fa" /> + <param name="type" value="specific" /> + <param name="tablesize_specific" value="1e7" /> + <param name="n_tables" value="2" /> + <param name="ksize" value="17" /> + <param name="no_zero" value="false" /> + <output name="output_histogram_filename"> + <assert_contents> + <has_text text="1 96 96 0.98" /> + <has_text text="1001 2 98 1.0" /> + </assert_contents> + </output> + </test> </tests> <!-- [OPTIONAL] Help displayed in Galaxy -->
--- a/filter-abund.xml Sun Jun 29 09:50:29 2014 -0400 +++ b/filter-abund.xml Sun Jun 29 10:28:09 2014 -0400 @@ -13,13 +13,13 @@ </macros> <expand macro="requirements" /> <command> - mkdir output; cd output; - filter-abund.py - $variable_coverage - $countingtable_to_load - #for input in $inputs - $input - #end for +mkdir output; cd output; +filter-abund.py +$variable_coverage +$countingtable_to_load +#for input in $inputs + $input +#end for </command> <inputs>
--- a/macros.xml Sun Jun 29 09:50:29 2014 -0400 +++ b/macros.xml Sun Jun 29 10:28:09 2014 -0400 @@ -20,7 +20,7 @@ <param name="type" type="select" label="Advanced Parameters" - help="ksize, n_hashess, a specific hashsize" > + help="ksize, n_tables, a specific tablesize" > <option value="simple" selected="true"> Hide @@ -30,7 +30,7 @@ </option> </param> <when value="simple"> - <param name="hashsize" + <param name="tablesize" type="select" label="Sample Type" display="radio"> @@ -55,16 +55,16 @@ value="20" label="ksize" help="k-mer size to use" /> - <param name="n_hashes" + <param name="n_tables" type="integer" min="1" value="4" - label="n_hashes" - help="number of hash tables to use" /> - <param name="hashsize_specifc" + label="n_tables" + help="number of tables to use" /> + <param name="tablesize_specifc" type="text" - label="hashsize" - help="lower bound on the hashsize to use" /> + label="tablesize" + help="lower bound on the tablesize to use" /> </when> </conditional> </xml>