# HG changeset patch
# User greg
# Date 1488467290 18000
# Node ID 34dcfb570551e394e9c82e78f84a79211e3e9691
# Parent  5f76ffe55d0f4049c85fb6af6a8e5d492dbe2098
Uploaded

diff -r 5f76ffe55d0f -r 34dcfb570551 phylogenomics_analysis.xml
--- a/phylogenomics_analysis.xml	Tue Feb 28 11:10:33 2017 -0500
+++ b/phylogenomics_analysis.xml	Thu Mar 02 10:08:10 2017 -0500
@@ -13,9 +13,6 @@
     </stdio>
     <command>
         <![CDATA[
-            #import os
-            #import sys
-
             #if str($options_type.options_type_selector) == 'advanced':
                 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
                 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
@@ -269,13 +266,13 @@
 
 **Options**
 
- * **Required options**
+ * **Required**
 
   - **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**
+ * **Multiple sequence alignments**
 
   - **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'.
@@ -283,7 +280,7 @@
   - **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**
 
   - **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.
@@ -291,7 +288,7 @@
   - **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**
 
   - **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.