changeset 5:31673ee3734f draft

Uploaded

--- a/assembly_post_processor.xml	Tue Jan 24 10:32:40 2017 -0500
+++ b/assembly_post_processor.xml	Fri Jan 27 15:03:00 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="1.0.0">
-    <description>pipeline</description>
+<tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3">
+    <description>into putative coding sequences</description>
     <requirements>
-        <requirement type="package" version="0.2">plant_tribes_assembly_post_processor</requirement>
+        <requirement type="package" version="0.3">plant_tribes_assembly_post_processor</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -112,8 +112,8 @@
     </tests>
     <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 post-processes de novo assembly
-transcripts into putative coding sequences and their corresponding amino acid translations.
+complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It postprocesses de novo assembly
+transcripts into putative coding sequences and their corresponding amino acid translations, locally assembling targeted gene families.
 
 -----
 
@@ -121,12 +121,12 @@
 
  * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
  * **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.  The next version of this tool will use a dynamic select list for this feature.
+ * **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.
- * **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL.
- * **Remove gappy sites in alignments** - 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.
+ * **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.
  * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
  * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.
  
@@ -134,7 +134,7 @@
     <citations>
             <citation type="bibtex">
                 @unpublished{None,
-                author = {None},
+                author = {Eric Wafula},
                 title = {None},
                 year = {None},
                 eprint = {None},