Mercurial > repos > crusoe > khmer
changeset 42:0f23e9402172
Include countingtable output for a-d-s
| author | Michael R. Crusoe <mcrusoe@msu.edu> |
|---|---|
| date | Mon, 30 Jun 2014 15:37:11 -0400 |
| parents | 1727dd6f7374 |
| children | bb3e059a53a8 |
| files | abundance-dist-single.xml filter-abund.xml macros.xml |
| diffstat | 3 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/abundance-dist-single.xml Mon Jun 30 12:20:45 2014 -0400 +++ b/abundance-dist-single.xml Mon Jun 30 15:37:11 2014 -0400 @@ -21,10 +21,11 @@ $zero $bigcount #if $save_countingtable ---savetable=$countingtable_to_save +--savetable=$optional_output_countingtable #end if --report-total-kmers --squash +@THREADS@ $input_sequence_filename $output_histogram_filename </command> @@ -45,6 +46,11 @@ <expand macro="tableinputs" /> </inputs> <outputs> + <data name="optional_output_countingtable" + format="ct" + label="${tool.name} k-mer counting table from #echo ', '.join(map(str, $inputs)))#"> + <filter>save_countingtable == True</filter> + </data> <expand macro="abundance-histogram-output" /> </outputs> <stdio>
--- a/filter-abund.xml Mon Jun 30 12:20:45 2014 -0400 +++ b/filter-abund.xml Mon Jun 30 15:37:11 2014 -0400 @@ -19,6 +19,7 @@ --cutoff=$cutoff #fi $variable_coverage +@THREADS@ $countingtable_to_load #for input in $inputs $input @@ -74,7 +75,7 @@ </output> </test> </tests> - <!-- [OPTIONAL] Help displayed in Galaxy --> + <!-- [OPTIONAL] ReST Help displayed in Galaxy --> <!-- <help> </help>
--- a/macros.xml Mon Jun 30 12:20:45 2014 -0400 +++ b/macros.xml Mon Jun 30 15:37:11 2014 -0400 @@ -14,7 +14,8 @@ --ksize=$parameters.ksize --n_tables=$parameters.n_tables --min-tablesize=$parameters.tablesize_specific -#end if</token> + #end if</token> + <token name="@THREADS@">--threads \$GALAXY_SLOTS</token> <xml name="tableinputs"> <conditional name="parameters"> <param name="type"