Mercurial > repos > crusoe > khmer
changeset 40:702ac46f423c
typo
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Mon, 30 Jun 2014 12:18:25 -0400 |
| parents | 31c05c5f7032 |
| children | 1727dd6f7374 |
| files | abundance-dist.xml normalize-by-median.xml |
| diffstat | 2 files changed, 19 insertions(+), 77 deletions(-) [+] |
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--- a/abundance-dist.xml Mon Jun 30 12:16:39 2014 -0400 +++ b/abundance-dist.xml Mon Jun 30 12:18:25 2014 -0400 @@ -55,8 +55,8 @@ <param name="no_zero" value="false" /> <output name="output_histogram_filename"> <assert_contents> - <has_line_matching="1 96 96 0.98" /> - <has_line_matching="255 2 98 1.0" /> + <has_line_matching expression="1 96 96 0.98" /> + <has_line_matching expression="255 2 98 1.0" /> </assert_contents> </output> </test>
--- a/normalize-by-median.xml Mon Jun 30 12:16:39 2014 -0400 +++ b/normalize-by-median.xml Mon Jun 30 12:18:25 2014 -0400 @@ -13,30 +13,22 @@ </macros> <expand macro="requirements" /> <command> - mkdir output; - cd output; - normalize-by-median.py - $paired_switch - #if $parameters.type == "simple" - --ksize=20 - --n_tables=4 - --min-tablesize=$parameters.tablesize - #else - --ksize=$parameters.ksize - --n_tables=$parameters.n_tables - --min-tablesize=$parameters.tablesize_specific - #end if - --cutoff=$cutoff - #if $save_countingtable - --savetable=$countingtable - #end if - #if $countingtable_to_load - --loadtable=$countingtable_to_load - #end if - --report-total-kmers - #for input in $inputs - $input - #end for +mkdir output; +cd output; +normalize-by-median.py +$paired_switch +@TABLEPARAMS@ +--cutoff=$cutoff +#if $save_countingtable +--savetable=$countingtable +#end if +#if $countingtable_to_load +--loadtable=$countingtable_to_load +#end if +--report-total-kmers +#for input in $inputs +$input +#end for </command> <inputs> @@ -64,57 +56,7 @@ min="1" value="20" label="cutoff" /> - <conditional name="parameters"> - <param name="type" - type="select" - label="Advanced Parameters" - help="ksize, n_tables, a specific tablesize" > - <option value="simple" - selected="true"> - Hide - </option> - <option value="specific"> - Show - </option> - </param> - <when value="simple"> - <param name="tablesize" - type="select" - label="Sample Type" - display="radio"> - <option value="1e9" - selected="true"> - Microbial Genome - </option> - <option value="2e9"> - Animal Transcriptome - </option> - <option value="4e9"> - Small Animal Genome or Low-Diversity Metagenome - </option> - <option value="16e9"> - Large Animal Genome - </option> - </param> - </when> - <when value="specific"> - <param name="ksize" - type="integer" - value="20" - label="ksize" - help="k-mer size to use" /> - <param name="n_tables" - type="integer" - min="1" - value="4" - label="n_tables" - help="number of k-mer counting tables to use" /> - <param name="tablesize_specific" - type="text" - label="tablesize" - help="lower bound on the tablesize to use" /> - </when> - </conditional> + <expand macro="tableinputs" /> </inputs> <outputs> <data name="countingtable"