# HG changeset patch
# User greg
# Date 1486989960 18000
# Node ID 63a4a0f127dadf07f28010fe7e1ee35e1f0948f2
# Parent  1e639e679f61996160839bbc46198b84cdca3117
Uploaded

diff -r 1e639e679f61 -r 63a4a0f127da assembly_post_processor.xml
--- a/assembly_post_processor.xml	Mon Feb 13 07:40:02 2017 -0500
+++ b/assembly_post_processor.xml	Mon Feb 13 07:46:00 2017 -0500
@@ -136,7 +136,7 @@
  * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
  * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
  * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
- * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the [Data Manager PlantTribes Scaffolds Downloader tool](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/4c96b684f0fd).
+ * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the `Data Manager PlantTribes Scaffolds Downloader tool<https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/>`_.
  * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
  * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
  * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.