Mercurial > repos > george-weingart > graphlan_import

comparison export2graphlan.xml @ 14:b084b394910e draft

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author george-weingart
date Thu, 04 Sep 2014 14:43:43 -0400
parents 66c50eadf709
children e743b0890ce2
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13:66c50eadf709 14:b084b394910e
7 -t $output_tree_file 7 -t $output_tree_file
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
13 --background_clades $background_clades
12 --skip_rows 1,2 14 --skip_rows 1,2
13 </command> 15 </command>
14 16
15 <inputs> 17 <inputs>
16 <param name="export_title" type="text" format="text" label="Title" value="Title"/>
17 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
18 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
19 <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"/> 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"/>
20 <param format="lefse_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/> 19 <param format="lefse_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
20 <param name="export_title" type="text" format="text" label="Title" value="Title"/>
21 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
22 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
23 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>
24 <param name="background_clades" type="text" format="text" label="Background Clades" />
25
26
21 </inputs> 27 </inputs>
22 <outputs> 28 <outputs>
23 <data name="output_annot_file" format="circl" /> 29 <data name="output_annot_file" format="circl" />
24 <data name="output_tree_file" format="circl" /> 30 <data name="output_tree_file" format="circl" />
25 </outputs> 31 </outputs>
38 44
39 * **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. 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.
40 46
41 * **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. 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.
42 48
43 Input parameters8888 49 Input parameters9999
44 -------------------- 50 --------------------
45 51
46 --annotations ANNOTATIONS 52 --annotations ANNOTATIONS
47 List which levels should be annotated in the tree. Use 53 List which levels should be annotated in the tree. Use
48 a comma separate values form, e.g., 54 a comma separate values form, e.g.,