Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 16:8c34d0d94c44 draft

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author george-weingart
date Thu, 04 Sep 2014 15:22:36 -0400
parents e743b0890ce2
children 33a3a37c7872
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15:e743b0890ce2 16:8c34d0d94c44
8 -a $output_annot_file 8 -a $output_annot_file
9 --title $export_title 9 --title $export_title
10 --annotations $export_annotations 10 --annotations $export_annotations
11 --external_annotations $export_external_annotations 11 --external_annotations $export_external_annotations
12 --background_levels $background_levels 12 --background_levels $background_levels
13 --background_clades $background_clades 13 #if $background_clades != " ":
14 --background_clades $background_clades
15 #end if
16
17
14 --skip_rows 1,2 18 --skip_rows 1,2
15 </command> 19 </command>
16 20
17 <inputs> 21 <inputs>
18 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse - See samples below - Please use Galaxy Get-Data/Upload-File. Use File-Type = Tabular" help="This is the file that was used as input for Lefse"/> 22 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse - See samples below - Please use Galaxy Get-Data/Upload-File. Use File-Type = Tabular" help="This is the file that was used as input for Lefse"/>
44 48
45 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value. 49 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value.
46 50
47 * **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. 51 * **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.
48 52
49 Input parameters9999 53 Input parameters1234
50 -------------------- 54 --------------------
51 55
52 --annotations ANNOTATIONS 56 --annotations ANNOTATIONS
53 List which levels should be annotated in the tree. Use 57 List which levels should be annotated in the tree. Use
54 a comma separate values form, e.g., 58 a comma separate values form, e.g.,