# HG changeset patch
# User greg
# Date 1485547412 18000
# Node ID 53f404994667645b10275c8c19be0950fbd8a4eb
# Parent  5423ad5c4f008ff567fd7fed625528ee71d891ee
Uploaded

diff -r 5423ad5c4f00 -r 53f404994667 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Tue Jan 24 10:33:16 2017 -0500
+++ b/phylogenomics_analysis.xml	Fri Jan 27 15:03:32 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="1.0.0">
-    <description>pipeline</description>
+<tool id="plant_tribes_phylogenomics_analysis" name="Perform phylogenomic analyses" version="0.3">
+    <description>by creating multiple sequence alignments and inferred maximum likelihood phylogenies</description>
     <requirements>
-        <requirement type="package" version="0.2">plant_tribes_phylogenomics_analysis</requirement>
+        <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -186,7 +186,7 @@
                     <when value="no" />
                     <when value="yes">
                         <conditional name="multiple_sequence_alignments_option_cond">
-                            <param name="multiple_sequence_alignments_option" label="Select process for multiple sequence alignments" type="select" force_select="True">
+                            <param name="multiple_sequence_alignments_option" label="Select method for multiple sequence alignments" type="select" force_select="True">
                                 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
                                 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
                                 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
@@ -308,7 +308,8 @@
     <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, comparing and analyzing the sequences of single genes, or a small number of genes, as well as many other types of data.
+analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produces by the
+**Classify gene sequences into precomputed orthologous gene family clusters** tool.
 
 -----
 
@@ -318,21 +319,21 @@
 
  - **Select sequences classified into gene family clusters** - A history item with the label 'Sequences classified into gene family clusters on...'.
  - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
- - **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
+ - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
 
 * **Multiple sequence alignments options**
 
- - **Select process for multiple sequence alignments** - Process used for setting multiple sequence alignments.
- - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
+ - **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 'Yes' was selected for the 'Create orthogroup fasta files?' option on the 'Classify gene sequences into precomputed orthologous gene family clusters' tool when generating the selected input.  This tool will produce an error if 'No' was selected.
  - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
- - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference.
- - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input.  This tool will produce an error if 'No' was selected.
+ - **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 'Yes' was selected for the 'Create corresponding coding sequences?' option on the 'Classify gene sequences into precomputed orthologous gene family clusters' tool when generating the selected input.  This tool will produce an error if 'No' was selected.
 
 * **Phylogenetic trees options**
 
  - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
  - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
- - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
+ - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** - History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
  - **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.
@@ -347,7 +348,7 @@
     <citations>
             <citation type="bibtex">
                 @unpublished{None,
-                author = {None},
+                author = {Eric Wafula},
                 title = {None},
                 year = {None},
                 eprint = {None},