# HG changeset patch
# User greg
# Date 1509371703 14400
# Node ID bb9f29c4a770be6e17357f87628b34b816c9544f
# Parent  f5bdcd2729cc2926c28a333ff75fc33c36debd5e
Uploaded

diff -r f5bdcd2729cc -r bb9f29c4a770 .shed.yml
--- a/.shed.yml	Thu Aug 24 13:45:41 2017 -0400
+++ b/.shed.yml	Mon Oct 30 09:55:03 2017 -0400
@@ -5,7 +5,7 @@
 homepage_url: https://github.com/dePamphilis/PlantTribes
 long_description: |
   Contains a tool that plots the distribution of synonymous substitution (Ks) rates and fits significant component(s).
-remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/ks_distribution
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/ks_distribution
 type: unrestricted
 categories:
 - Phylogenetics
diff -r f5bdcd2729cc -r bb9f29c4a770 ks_distribution.xml
--- a/ks_distribution.xml	Thu Aug 24 13:45:41 2017 -0400
+++ b/ks_distribution.xml	Mon Oct 30 09:55:03 2017 -0400
@@ -1,9 +1,11 @@
-<tool id="ks_distribution" name="KsDistribution" version="@WRAPPER_VERSION@.2">
+<tool id="ks_distribution" name="KsDistribution" version="@WRAPPER_VERSION@.3.0">
     <description>plots the distribution of synonymous substitution (Ks) rates and fits significant component(s)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements_ks_distribution" />
+    <requirements>
+        <requirement type="package" version="1.3.2">r-optparse</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/ks_distribution.R'
 -k '$input'
@@ -21,7 +23,7 @@
     ]]></command>
     <inputs>
         <param name="input" format="tabular" type="data" label="KaKsAnalysis tabular file" />
-        <param name="components" format="ptkscmp" type="data" label="Significant components" />
+        <param name="components" format="tabular" type="data" label="Significant components" />
         <conditional name="choose_colors_cond">
             <param name="choose_colors" type="select" label="Choose colors for significant components">
                 <option value="no" selected="true">No</option>
diff -r f5bdcd2729cc -r bb9f29c4a770 macros.xml
--- a/macros.xml	Thu Aug 24 13:45:41 2017 -0400
+++ b/macros.xml	Mon Oct 30 09:55:03 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,