Mercurial > repos > crusoe > khmer
changeset 26:de12b461034f
fix nobigcount
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Sun, 29 Jun 2014 13:01:27 -0400 |
| parents | f2151b15d0b6 |
| children | e6b1ef398fc8 |
| files | abundance-dist-single.xml abundance-dist.xml macros.xml test-data/test-abund-read-2.nobigcount.ct |
| diffstat | 4 files changed, 15 insertions(+), 11 deletions(-) [+] |
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--- a/abundance-dist-single.xml Sun Jun 29 12:51:01 2014 -0400 +++ b/abundance-dist-single.xml Sun Jun 29 13:01:27 2014 -0400 @@ -35,12 +35,7 @@ type="boolean" label="Save the k-mer counting table(s) in a file" help="" /> - <param name="zero" - type="boolean" - truevalue="" - falsevalue="--no-zero" - checked="true" - help="Output zero count bins" /> + <expand macron="input_zero" /> <param name="bigcount" type="boolean" truevalue=""
--- a/abundance-dist.xml Sun Jun 29 12:51:01 2014 -0400 +++ b/abundance-dist.xml Sun Jun 29 13:01:27 2014 -0400 @@ -17,14 +17,16 @@ ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces mkdir output; cd output; @BINARY@ - $input_counting_table_filename - $input_sequence_filename - $output_histogram_filename +--squash +$input_counting_table_filename +$input_sequence_filename +$output_histogram_filename </command> <inputs> <expand macro="input_sequence_filename" /> <expand macro="input_counting_table_filename" /> + <expand macro="input_zero" /> </inputs> <outputs> <expand macro="abundance-histogram-output" /> @@ -49,9 +51,8 @@ </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="input_counting_table_filename" value="test-abund-read-2.nobigcount.ct" /> <param name="no_zero" value="false" /> - <param name="no_bigcount" value="false" /> <output name="output_histogram_filename"> <assert_contents> <has_text text="1 96 96 0.98" />
--- a/macros.xml Sun Jun 29 12:51:01 2014 -0400 +++ b/macros.xml Sun Jun 29 13:01:27 2014 -0400 @@ -104,4 +104,12 @@ <discover_datasets pattern="__name__" directory="output" visible="true"/> </data> </xml> + <xml name="input_zero"> + <param name="zero" + type="boolean" + truevalue="" + falsevalue="--no-zero" + checked="true" + help="Output zero count bins" /> + </xml> `</macros>