# HG changeset patch
# User greg
# Date 1493384929 14400
# Node ID 5de0658ef8846fd67857c89293d9362405587df9
# Parent  b2ae23e484e80b482db1518ff800456c389a6998
Uploaded

diff -r b2ae23e484e8 -r 5de0658ef884 gene_family_classifier.xml
--- a/gene_family_classifier.xml	Tue Apr 11 14:24:23 2017 -0400
+++ b/gene_family_classifier.xml	Fri Apr 28 09:08:49 2017 -0400
@@ -1,5 +1,5 @@
 <tool id="plant_tribes_gene_family_classifier" name="GeneFamilyClassifier" version="@WRAPPER_VERSION@.0">
-    <description>classifies gene sequences into pre-computed orthologous plant gene family clusters</description>
+    <description>classifies gene sequences into pre-computed orthologous gene family clusters</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -250,8 +250,8 @@
 the AssemblyPostProcessor tool or from an external source into pre-computed orthologous gene family clusters (orthogroups)
 of a PlantTribes scaffold.  Classified sequences are then assigned with the corresponding orthogroups’ metadata that includes
 gene counts of backbone taxa, super clusters (super orthogoups) at multiple stringencies, and functional annotations from
-sources such as Gene Ontology (GO), InterPro protein domains, and UniProt KB/Swiss-Prot.  Additionally, sequences belonging
-to single/low-copy gene families that are mainly utilized in species tree inference can be determined.
+sources such as Gene Ontology (GO), InterPro protein domains, TAIR, UniProtKB/TrEMBL, and UniProtKB/Swiss-Prot.  Additionally,
+sequences belonging to single/low-copy gene families that are mainly utilized in species tree inference can be determined.
 
 -----
 
@@ -290,7 +290,34 @@
     </help>
     <citations>
         <expand macro="citation1" />
-        <expand macro="citations2to4" />
+        <citation type="bibtex">
+            @article{Sasidharan2012,
+            journal = {Nucleic Acids Research},
+            author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
+            title = {GFam: a platform for automatic annotation of gene families},
+            year = {2012},
+            pages = {gks631},}
+        </citation>
+        <citation type="bibtex">
+            @article{Li2003,
+            journal = {Genome Research}
+            author = {3. Li L, Stoeckert CJ, Roos DS},
+            title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
+            year = {2003},
+            volume = {13},
+            number = {9},
+            pages = {2178-2189},}
+        </citation>
+        <citation type="bibtex">
+            @article{Emms2015,
+            journal = {Genome Biology}
+            author = {4. Emms DM, Kelly S},
+            title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
+            year = {2015},
+            volume = {16},
+            number = {1},
+            pages = {157},}
+        </citation>
         <citation type="bibtex">
             @article{Altschul1990,
             journal = {Journal of molecular biology}
diff -r b2ae23e484e8 -r 5de0658ef884 macros.xml
--- a/macros.xml	Tue Apr 11 14:24:23 2017 -0400
+++ b/macros.xml	Fri Apr 28 09:08:49 2017 -0400
@@ -3,7 +3,7 @@
     <token name="@WRAPPER_VERSION@">0.8</token>
     <xml name="requirements_assembly_post_processor">
         <requirements>
-            <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
+            <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
         </requirements>
     </xml>
     <xml name="requirements_gene_family_aligner">
@@ -59,13 +59,13 @@
         </param>
     </xml>
     <xml name="param_orthogroup_fna">
-        <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
+        <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences?">
             <option value="yes" selected="true">Yes</option>
             <option value="no">No</option>
         </param>
     </xml>
     <xml name="param_scaffold">
-        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
+        <param name="scaffold" type="select" label="Gene family scaffold">
             <options from_data_table="plant_tribes_scaffolds" />
             <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
         </param>
@@ -78,9 +78,9 @@
     </xml>
     <xml name="cond_alignment_method">
         <conditional name="alignment_method_cond">
-            <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
-                <option value="mafft" selected="true">MAFFT algorithm</option>
-                <option value="pasta">PASTA algorithm</option>
+            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
+                <option value="mafft" selected="true">MAFFT</option>
+                <option value="pasta">PASTA</option>
             </param>
             <when value="mafft" />
             <when value="pasta">
@@ -90,31 +90,31 @@
     </xml>
     <xml name="cond_remove_gappy_sequences">
         <conditional name="remove_gappy_sequences_cond">
-            <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
+            <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration?">
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no" />
             <when value="yes">
                 <conditional name="trim_type_cond">
-                    <param name="trim_type" type="select" label="Select process used for trimming">
-                        <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
-                        <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
+                    <param name="trim_type" type="select" label="Trimming method">
+                        <option value="gap_trimming" selected="true">Gap score based trimming</option>
+                        <option value="automated_trimming">Automated heuristic trimming</option>
                     </param>
                     <when value="gap_trimming">
-                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
+                        <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
                     </when>
                     <when value="automated_trimming" />
                 </conditional>
                 <conditional name="remove_sequences_with_gaps_cond">
-                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
+                    <param name="remove_sequences_with_gaps" type="select" label="Remove sequences?">
                         <option value="no" selected="true">No</option>
                         <option value="yes">Yes</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
-                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
+                        <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
+                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
                     </when>
                 </conditional>
             </when>
@@ -130,34 +130,4 @@
             url = {https://github.com/dePamphilis/PlantTribes},}
         </citation>
     </xml>
-    <xml name="citations2to4">
-        <citation type="bibtex">
-            @article{Sasidharan2012,
-            journal = {Nucleic Acids Research},
-            author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
-            title = {GFam: a platform for automatic annotation of gene families},
-            year = {2012},
-            pages = {gks631},}
-        </citation>
-        <citation type="bibtex">
-            @article{Li2003,
-            journal = {Genome Research}
-            author = {3. Li L, Stoeckert CJ, Roos DS},
-            title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
-            year = {2003},
-            volume = {13},
-            number = {9},
-            pages = {2178-2189},}
-        </citation>
-        <citation type="bibtex">
-            @article{Emms2015,
-            journal = {Genome Biology}
-            author = {4. Emms DM, Kelly S},
-            title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
-            year = {2015},
-            volume = {16},
-            number = {1},
-            pages = {157},}
-        </citation>
-    </xml>
 </macros>
diff -r b2ae23e484e8 -r 5de0658ef884 repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Fri Apr 28 09:08:49 2017 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="This tool uses the data installed by the data_manager_plant_tribes_scaffolds_downloader Data Manager tool.">
+    <repository changeset_revision="8bb32fd5b175" name="data_manager_plant_tribes_scaffolds_downloader" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>