Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH with parsing Qiime
Created: 2013-05-07 12:13:37
Last updated: 2015-06-12 13:39:38
Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH .
The WF need a tree in newick format, a samplefile that show the where the leaf of the tree are found in the different sample and how many time, and a grouping file where the different sample are grouped using a categorical variable. The WF gives back a tabular and graphical representation of an entropy based partitioning of the information present in the sequence across the groupings, and a graphical and tabular representation of the contribution of each branch of the tree to the differentiation across groups of sample.
Further as side results the WF gives the tree annotated with the per branch contribution to the differentiation across groups of sample in nexml or phyloxml format and all files necessary to produce ex.novo the annotated tree on itol, giving the possibility to the user to add taxonomic information.
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Authors (1)
| saverio vicario
giacinto Donvito
alfonso monaco
|
Titles (1)
| Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH with parsing Quime |
Descriptions (1)
| Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH .
The WF need a tree in newick format, a samplefile that show the where the leaf of the tree are found in the different sample and how many time, and a grouping file where the different sample are grouped using a categorical variable. The WF gives back a tabular and graphical representation of an entropy based partitioning of the information present in the sequence across the groupings, and a graphical and tabular representation of the contribution of each branch of the tree to the differentiation across groups of sample.
Further as side results the WF gives the tree annotated with the per branch contribution to the differentiation across groups of sample in nexml or phyloxml format and all files necessary to produce ex.novo the annotated tree on itol, giving the possibility to the user to add taxonomic information.
|
Dependencies (0)
Inputs (10)
| Name |
Description |
| TreeFile |
phylogenetic infernece in newick format of the sequences ( or clusters of sequences ) present in the different samples. Internal label are overwritten by the service.
|
| randomization |
insert an integer to define number of randomization to perform to estimate significance of the difference found across groups. Good rule of the thumb randomization = nlog(n) where n is the number of sequences.
|
| qparamHill |
float larger than zero, define the diversity index to be used following Hill parametrization. 1 is shannon index
|
| outputPrefix |
Prefix for all outputfiles
|
| xmloutputType |
Type of xml summary output type: two possible standard are used nexml and phyloxml. T
At the moment phyloxml is fully supported while nexml have some possible error
|
| Seq_otus |
Clustering file produced by Usearch within Quime pipeline
|
| MappingFile |
|
| DataSelection_Map_Column |
Data selection using a state (defined elsewhere ) within the map file on the column here defined
possible values:
'Status', 'Probe', 'Organism', 'Site', 'Description'
|
| DataSelection_Map_State |
Select data based on the state here defined on the column of the map file defined elsewhere
Input file is a string
|
| CategoricalVariable_Map_column |
Categorical variable to be used to partition sequence information.
the variable need to be defined within the map file selecting one of this possible columns name
'Status', 'Probe', 'Organism', 'Site', 'Description'
|
Processors (11)
| Name |
Type |
Description |
| Call_Retrieve_PhyloH |
workflow |
|
| Upload_tree |
workflow |
|
| Upload_sample |
workflow |
|
| Upload_sample_grouping |
workflow |
|
| FormInput2PhyloH |
localworker |
Scriptoutput = tree +" "+sample +" "+group +" "+Nrandomization +" "+qparamHill +" "+output_prefix +" "+XMLoutputType; |
| ServiceName |
stringconstant |
ValuePhyloH |
| File_name_value |
stringconstant |
Valuegroup |
| File_name_value_1 |
stringconstant |
Valuesample |
| File_name_value_2 |
stringconstant |
Valuetree |
| Interaction |
interaction |
|
| Tool |
externaltool |
|
Outputs (3)
| Name |
Description |
| JobID |
integer that identify the job on the farm. Use it with the service centre to find out bug or crash of the job
|
| OutputPath |
Link to folder with all details of estimation
|
| StandardOuput |
URL of the HTML file of summary
|
Datalinks (24)
| Source |
Sink |
| FormInput2PhyloH:output |
Call_Retrieve_PhyloH:Argument |
| ServiceName:value |
Call_Retrieve_PhyloH:Name |
| TreeFile |
Upload_tree:InputBody |
| File_name_value_2:value |
Upload_tree:File_name |
| File_name_value_1:value |
Upload_sample:File_name |
| Tool:Samples |
Upload_sample:InputBody |
| File_name_value:value |
Upload_sample_grouping:File_name |
| Tool:Groups |
Upload_sample_grouping:InputBody |
| Upload_sample_grouping:REST_Service_redirection |
FormInput2PhyloH:group |
| Upload_sample:REST_Service_redirection |
FormInput2PhyloH:sample |
| Upload_tree:REST_Service_redirection |
FormInput2PhyloH:tree |
| randomization |
FormInput2PhyloH:Nrandomization |
| qparamHill |
FormInput2PhyloH:qparamHill |
| xmloutputType |
FormInput2PhyloH:XMLoutputType |
| outputPrefix |
FormInput2PhyloH:output_prefix |
| Call_Retrieve_PhyloH:Stadardouput |
Interaction:destination |
| MappingFile |
Tool:map |
| DataSelection_Map_Column |
Tool:map_column |
| CategoricalVariable_Map_column |
Tool:map_column2 |
| Seq_otus |
Tool:seq_otus |
| DataSelection_Map_State |
Tool:state_map_column |
| Call_Retrieve_PhyloH:JobID |
JobID |
| Call_Retrieve_PhyloH:Output_Path |
OutputPath |
| Call_Retrieve_PhyloH:Stadardouput |
StandardOuput |
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