# HG changeset patch
# User greg
# Date 1487358043 18000
# Node ID 6e859426c8731bcc31f1b5a3c2389f58d8aa800e
# Parent  e8a8650c7165ecc7f1912ca9f41d6b3434949e08
Uploaded

diff -r e8a8650c7165 -r 6e859426c873 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Fri Feb 17 13:05:55 2017 -0500
+++ b/gene_family_classifier.xml	Fri Feb 17 14:00:43 2017 -0500
@@ -189,19 +189,19 @@
                     <when value="no"/>
                     <when value="yes">
                         <conditional name="single_copy_cond">
-                            <param name="single_copy" type="select" label="Select single copy configuration">
+                            <param name="single_copy" type="select" label="Select single copy orthogroup configuration option">
                                 <option value="custom" selected="true">Single copy orthogroup custom configuration</option>
                                 <option value="taxa">Minimum single copy taxa required in orthogroup</option>
                             </param>
                             <when value="custom">
                                 <conditional name="single_copy_custom_cond">
-                                    <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration?" help="Select No to use the default configuration">
+                                    <param name="single_copy_custom" type="select" label="Select single copy orthogroup custom configuration from the current history?" help="Select No to use the default configuration">
                                         <option value="no" selected="true">No</option>
                                         <option value="yes">Yes</option>
                                     </param>
                                     <when value="no"/>
                                     <when value="yes">
-                                        <param name="single_copy_custom_config" format="txt" type="data" label="Select single copy custom configuration file"/>
+                                        <param name="single_copy_custom_config" format="txt" type="data" label="Single copy orthogroup custom configuration file"/>
                                     </when>
                                 </conditional>
                             </when>
@@ -293,7 +293,8 @@
  * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
  * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
  * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
- * **Specify single copy orthogroup selection?** - Select 'Yes' to specify 'Minimum single copy taxa required in orthogroup'.
+ * **Specify single copy orthogroup selection?** - Specify a single copy orthogroup custom configuration or the minimum single copy taxa required in the orthogroup.
+ * **Select single copy orthogroup custom configuration from the current history?** - If a custom configuration is chosen, the configuration can be selected from the current history or the default configuration can be used.
  * **Minimum single copy taxa required in orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
  * **Minimum taxa required in single copy orthogroup** - Used with "Minimum single copy taxa required in orthogroup" configuration only.
  * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".