changeset 59:963f84101cdc draft

Uploaded

--- a/phylogenomics_analysis.xml	Mon Feb 13 09:33:37 2017 -0500
+++ b/phylogenomics_analysis.xml	Wed Feb 15 07:59:49 2017 -0500
@@ -300,41 +300,42 @@
         </test>
     </tests>
     <help>
-        This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
-        complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
-        analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
-        **Classify gene sequences into precomputed orthologous gene family clusters** tool.
+This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
+analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
+**Classify gene sequences into precomputed orthologous gene family clusters** tool.
 
-        -----
+-----
 
-        **Options**
+**Options**
 
-        * **Required options**
+ * **Required options**
 
-        - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
-        - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
-        - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).  
-        * **Multiple sequence alignments options**
+  - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
+  - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
+  - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).  
+
+ * **Multiple sequence alignments options**
 
-        - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
-        - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
-        - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
-        - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
-        - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
+  - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
+  - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
+  - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
+  - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
+  - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
 
-        * **Phylogenetic trees options**
+ * **Phylogenetic trees options**
 
-        - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
-        - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
-        - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
-        - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
-        - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
+  - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
+  - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
+  - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
+  - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
+  - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
 
-        * **MSA quality control options**
+ * **MSA quality control options**
 
-        - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
-        - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
-        - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
+  - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
+  - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
+  - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
 
     </help>
     <citations>