Mercurial > repos > george-weingart > graphlan_import
changeset 54:c4fd494f5fa5 draft
Uploaded
| author | george-weingart |
|---|---|
| date | Sat, 06 Sep 2014 15:20:20 -0400 |
| parents | e0ab17903d9d |
| children | 5f8d50842c4f |
| files | import2graphlan.xml |
| diffstat | 1 files changed, 38 insertions(+), 11 deletions(-) [+] |
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--- a/import2graphlan.xml Sat Sep 06 15:15:42 2014 -0400 +++ b/import2graphlan.xml Sat Sep 06 15:20:20 2014 -0400 @@ -107,23 +107,34 @@ * **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 parameters1234 -==================== - - **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None - +Input parameters +================ + **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None + + + + **--external_annotations** EXTERNAL_ANNOTATIONS - List which levels should use the external legend for the annotation. Use a comma separate values form, e.g., --annotation_levels 1,2,3. Default is None - - + List which levels should use the external legend for the annotation. Use a comma separate values form, + e.g., --annotation_levels 1,2,3. Default is None + + + + **--background_levels** BACKGROUND_LEVELS - List which levels should be highlight with a shaded background. Use a comma separate values form, e.g.,--background_levels 1,2,3<br><br> + List which levels should be highlight with a shaded + background. Use a comma separate values form, e.g., + --background_levels 1,2,3 **--background_clades** BACKGROUND_CLADES Specify the clades that should be highlight with a shaded background. Use a comma separate values form and surround the string with " if it contains spaces. - Example: --background_clades "Bacteria.Actinobacteria, Bacteria.Bacteroidetes.Bacteroidia,Bacteria.Firmicutes.Clostridia.Clostridiales" + Example: --background_clades "Bacteria.Actinobacteria, + Bacteria.Bacteroidetes.Bacteroidia, + Bacteria.Firmicutes.Clostridia.Clostridiales" + + **--background_colors** BACKGROUND_COLORS @@ -132,6 +143,9 @@ Example: #29cc36, (150; 100; 100), (280;80; 88) + + + **--title TITLE** If specified set the title of the GraPhlAn plot. Surround the string with " if it contains spaces, e.g., --title "Title example" @@ -149,6 +163,7 @@ Default is 20 + **--max_clade_size** MAX_CLADE_SIZE Set the maximum value of clades that are biomarkers. Default is 200 @@ -158,10 +173,14 @@ Set a default font size. Default is 10 + + **--min_font_size** MIN_FONT_SIZE Set the minimum font size to use. Default is 8 + + **--max_font_size** MAX_FONT_SIZE Set the maximum font size. Default is 12 @@ -170,21 +189,28 @@ Set the font size for the annotation legend. Default is 10 + + **--abundance_threshold** ABUNDANCE_THRESHOLD Set the minimun abundace value for a clade to be annotated. Default is 20.0 + + **--most_abundant** MOST_ABUNDANT When only lefse_input is provided, you can specify how many clades highlight. Since the biomarkers are missing, they will be chosen from the most abundant + + **--least_biomarkers** LEAST_BIOMARKERS When only lefse_input is provided, you can specify the minimum number of biomarkers to extract. The taxonomy is parsed, and the level is choosen in order to have at least the specified number of biomarkers - + + **--discard_otus** If specified the OTU ids will be discarded from the taxonmy. Default behavior keep OTU ids in taxonomy @@ -235,3 +261,4 @@ .. _here: https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial </help> </tool> +