# HG changeset patch
# User greg
# Date 1507227947 14400
# Node ID 1938f0ed62792454f760d8525b7029bf3d239a91
# Parent  9b7b4f9d64de20384008f6b714279fccd72dc7d3
Uploaded

diff -r 9b7b4f9d64de -r 1938f0ed6279 .shed.yml
--- a/.shed.yml	Thu Aug 24 13:38:15 2017 -0400
+++ b/.shed.yml	Thu Oct 05 14:25:47 2017 -0400
@@ -8,7 +8,7 @@
   utilize objective classifications of complete protein sequences from sequenced plant genomes to perform
   comparative evolutionary studies.  This tool performs orthologous or paralogous ks analyses of coding sequences
   and amino acid sequences.
-remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/kaks_analysis
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/kaks_analysis
 type: unrestricted
 categories:
 - Phylogenetics
diff -r 9b7b4f9d64de -r 1938f0ed6279 kaks_analysis.xml
--- a/kaks_analysis.xml	Thu Aug 24 13:38:15 2017 -0400
+++ b/kaks_analysis.xml	Thu Oct 05 14:25:47 2017 -0400
@@ -1,9 +1,11 @@
-<tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_kaks_analysis" name="KaKsAnalysis" version="@WRAPPER_VERSION@.3.0">
     <description>estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements_kaks_analysis" />
+    <requirements>
+        <requirement type="package" version="1.0.3">plant_tribes_kaks_analysis</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #set output_dir = 'kaksAnalysis_dir'
 #set comparison = $comparison_cond.comparison
diff -r 9b7b4f9d64de -r 1938f0ed6279 macros.xml
--- a/macros.xml	Thu Aug 24 13:38:15 2017 -0400
+++ b/macros.xml	Thu Oct 05 14:25:47 2017 -0400
@@ -1,47 +1,6 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
     <token name="@WRAPPER_VERSION@">1.0</token>
-    <xml name="requirements_assembly_post_processor">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_aligner">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_classifier">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_integrator">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_kaks_analysis">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_ks_distribution">
-        <requirements>
-            <requirement type="package" version="1.3.2">r-optparse</requirement>
-        </requirements>
-    </xml>
-    <xml name="requirements_gene_family_phylogeny_builder">
-        <requirements>
-            <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement>
-        </requirements>
-    </xml>
-    <xml name="param_codon_alignments">
-        <param name="codon_alignments" type="select" label="Codon alignments">
-            <option value="yes" selected="true">Yes</option>
-            <option value="no">No</option>
-        </param>
-    </xml>
     <xml name="param_method">
         <param name="method" type="select" label="Protein clustering method">
             <option value="gfam" selected="true">GFam</option>
@@ -49,74 +8,12 @@
             <option value="orthomcl">OrthoMCL</option>
         </param>
     </xml>
-    <xml name="param_options_type">
-        <param name="options_type" type="select" label="Options Configuration">
-            <option value="basic" selected="true">Basic</option>
-            <option value="advanced">Advanced</option>
-        </param>
-    </xml>
-    <xml name="param_orthogroup_fna">
-        <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="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>
     </xml>
-    <xml name="param_sequence_type">
-        <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
-            <option value="protein" selected="true">Amino acid based</option>
-            <option value="dna">Nucleotide based</option>
-        </param>
-    </xml>
-    <xml name="cond_alignment_method">
-        <conditional name="alignment_method_cond">
-            <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">
-                <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
-            </when>
-        </conditional>
-    </xml>
-    <xml name="cond_remove_gappy_sequences">
-        <conditional name="remove_gappy_sequences_cond">
-            <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="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="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">
-                        <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="Coverage score" />
-                        <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-    </xml>
     <xml name="citation1">
         <citation type="bibtex">
             @misc{None,