Mercurial > repos > greg > gene_family_phylogeny_builder

changeset 11:0307ab4f5031 draft

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Uploaded
author greg
date Mon, 01 May 2017 11:21:10 -0400
parents 576278ba0dc4
children 1bebfea6d0b6
files gene_family_phylogeny_builder.xml
diffstat 1 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/gene_family_phylogeny_builder.xml	Mon May 01 09:17:16 2017 -0400
+++ b/gene_family_phylogeny_builder.xml	Mon May 01 11:21:10 2017 -0400
@@ -122,7 +122,7 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
+                        <param name="rooting_order" format="txt" type="data" label="Rooting order configuration" />
                     </when>
                 </conditional>
                 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Bootstrap replicates" />
@@ -152,15 +152,15 @@
 
  * **Orthogroup alignments** - orthogroup alignment fasta files produced by the GeneFamilyAligner tool selected from your history.  Depending on how the GeneFamilyAligner tool was executed, these could either be pre-processed alignments, trimmed alignments or both trimmed and filtered alignments.
  * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool.
- * **Protein clustering method** - gene family scaffold protein clustering method as described in the Asse3mblyPostProcessor tool.
+ * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
  * **Phylogenetic inference method** - method for estimating orthogroup maximum likelihood (ML) phylogenetic trees.  PlantTribes estimates ML phylogenetic trees using either RAxML or FastTree algorithms.
 
 **Other options**
 
  * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML.  Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_.  Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
  * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100).
- * **Maximum orthogroup size** - Maximum number of sequences allowed in orthogroup alignments (default = 100).
- * **Minimum orthogroup size** - Minimum number of sequences allowed in orthogroup alignments (default = 4).
+ * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100).
+ * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4).
 
 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config