Mercurial > repos > george-weingart > graphlan_import
changeset 21:5ecece9f42dd draft
Uploaded
| author | george-weingart |
|---|---|
| date | Thu, 04 Sep 2014 16:34:51 -0400 |
| parents | 65bf0d7f535b |
| children | b43531754e71 |
| files | export2graphlan.xml |
| diffstat | 1 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/export2graphlan.xml Thu Sep 04 16:19:09 2014 -0400 +++ b/export2graphlan.xml Thu Sep 04 16:34:51 2014 -0400 @@ -28,6 +28,9 @@ --max_font_size $max_font_size --annotation_legend_font_size $annotation_legend_font_size --abundance_threshold $abundance_threshold + #if $most_abundant > 0: + --most_abundant $most_abundant + #end if --skip_rows 1,2 </command> @@ -49,8 +52,9 @@ <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/> <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/> <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/> + <param name="most_abundant" type="integer" size="4" value="0" label=" When only lefse_input is provided, you can specify how many clades to highlight "/> - + least_biomarkers </inputs> <outputs> <data name="output_annot_file" format="circl" /> @@ -73,8 +77,8 @@ * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers. -Input parameters6666 --------------------- +Input parameters +---------------- --annotations ANNOTATIONS List which levels should be annotated in the tree. Use @@ -145,7 +149,7 @@ the internal nodes input parameters: - You need to provide at least LEfSe input data + -i LEFSE_INPUT, --lefse_input LEFSE_INPUT -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT