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changeset 0:5ace8af6edb6 draft

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Uploaded
author greg
date Mon, 01 May 2017 13:47:20 -0400
parents
children 7c0f41432772
files .shed.yml ks_distribution.R ks_distribution.xml macros.xml test-data/components.tabular test-data/output.pdf test-data/rates.tabular
diffstat 7 files changed, 534 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,11 @@
+name: plant_tribes_ks_distribution
+owner: greg
+description: |
+  Contains a tool that plots the distribution of synonymous substitution (Ks) rates and fits significant component(s).
+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
+type: unrestricted
+categories:
+- Phylogenetics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ks_distribution.R	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,115 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
+    make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
+    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
+args <- parse_args(parser, positional_arguments=TRUE)
+opt <- args$options
+
+
+get_num_components = function(components_data)
+{
+    # Get the max of the number_comp column.
+    number_comp = components_data[, 3]
+    num_components <- max(number_comp, na.rm=TRUE);
+    num_components
+}
+
+get_pi_mu_var = function(components_data, num_components)
+{
+    # FixMe: enhance this to generically handle any integer value for num_components.
+    if (num_components == 1)
+    {
+        pi <- c(components_data[1, 9]);
+        mu <- c(components_data[1, 7]);
+        var <- c(components_data[1, 8]);
+    }
+    else if (num_components == 2)
+    {
+        pi <- c(components_data[2, 9], components_data[3, 9]);
+        mu <- c(components_data[2, 7], components_data[3, 7]);
+        var <- c(components_data[2, 8], components_data[3, 8]);
+    }
+    else if (num_components == 3)
+    {
+        pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9]);
+        mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7]);
+        var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8]);
+    }
+    else if (num_components == 4)
+    {
+        pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9]);
+        mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7]);
+        var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8]);
+    }
+    return = c(pi, mu, var)
+    return
+}
+
+plot_ks<-function(kaks_input, output, pi, mu, var)
+{
+    # Start PDF device driver to save charts to output.
+    pdf(file=output, bg="white")
+    # Change bin width
+    bin <- 0.05 * seq(0, 40);
+    kaks <- read.table(file=kaks_input, header=T);
+    kaks <- kaks[kaks$Ks<2,];
+    h.kst <- hist(kaks$Ks, breaks=bin, plot=F);
+    nc <- h.kst$counts;
+    vx <- h.kst$mids;
+    ntot <- sum(nc);
+    # Set margin for plot bottom, left top, right.
+    par(mai=c(0.5, 0.5, 0, 0));
+    # Plot dimension in inches.
+    par(pin=c(2.5, 2.5));
+    g <- calculate_fitted_density(pi, mu, var);
+    h <- ntot * 2.5 / sum(g);
+    vx <- seq(1, 100) * 0.02;
+    ymax <- max(nc) + 5;
+    barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0,2), ylim=c(0, ymax));
+    # Add x-axis.
+    axis(1);
+    color <- c('green', 'blue', 'black', 'red');
+    for (i in 1:length(mu))
+    {
+       lines(vx, g[,i] * h, lwd=2, col=color[i]);
+    }
+};
+
+calculate_fitted_density <- function(pi, mu, var)
+{
+    comp <- length(pi);
+    var <- var/mu^2;
+    mu <- log(mu);
+    #calculate lognormal density
+    vx <- seq(1, 100) * 0.02;
+    fx <- matrix(0, 100, comp);
+    for (i in 1:100)
+    {
+        for (j in 1:comp)
+        {
+           fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])));
+        };
+     };
+    fx;
+}
+
+# Read in the components data.
+components_data <- read.delim(opt$components_input, header=TRUE);
+# Get the number of components.
+num_components <- get_num_components(components_data)
+
+# Set pi, mu, var.
+items <- get_pi_mu_var(components_data, num_components);
+pi <- items[1];
+mu <- items[2];
+var <- items[3];
+
+# Plot the output.
+plot_ks(opt$kaks_input, opt$output, pi, mu, var);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ks_distribution.xml	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,110 @@
+<tool id="ks_distribution" name="KsDistribution" version="1.0.0">
+    <description>plots the distribution of synonymous substitution (Ks) rates and fits significant componets(s)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements_ks_distribution" />
+    <expand macro="stdio" />
+    <command>
+        <![CDATA[
+            Rscript $__tool_directory__/ks_distribution.R
+            -k '${kaks}'
+            -c '${components}'
+            -o '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="rates" format="tabular" type="data" label="Synonymous substitution rates" />
+        <param name="components" format="tabular" type="data" label="Significant components" />
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rates" value="rates.tabular" ftype="tabular" />
+            <param name="components" value="components.tabular" ftype="tabular" />
+            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+ 
+This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
+genome-scale gene families and transcriptomes.  This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
+distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
+
+-----
+
+**Options**
+
+ * **Required**
+
+  - **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
+  - **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
+    </help>
+    <citations>
+        <expand macro="citation1" />
+        <citation type="bibtex">
+            @article{Wall2008,
+            journal = {Nucleic Acids Research},
+            author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
+            title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
+            year = {2008},
+            volume = {36},
+            number = {suppl 1},
+            pages = {D970-D976},}
+        </citation>
+        <citation type="bibtex">
+            @article{Altschul1990,
+            journal = {Journal of molecular biology}
+            author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
+            title = {Basic local alignment search tool},
+            year = {1990},
+            volume = {215},
+            number = {3},
+            pages = {403-410},}
+        </citation>
+        <citation type="bibtex">
+            @article{Katoh2013,
+            journal = {Molecular biology and evolution},
+            author = {4. Katoh K, Standley DM},
+            title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
+            year = {2013},
+            volume = {30},
+            number = {4},
+            pages = {772-780},}
+        </citation>
+        <citation type="bibtex">
+            @article{Yang2007,
+            journal = {Molecular biology and evolution},
+            author = {5. Yang Z},
+            title = {PAML 4: phylogenetic analysis by maximum likelihood},
+            year = {2007},
+            volume = {24},
+            number = {8},
+            pages = {1586-1591},}
+        </citation>
+        <citation type="bibtex">
+            @article{Cui2006,
+            journal = {Genome Research},
+            author = {6. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},
+            title = {Widespread genome duplications throughout the history of flowering plants},
+            year = {2006},
+            volume = {16},
+            number = {6},
+            pages = {738-749},}
+        </citation>
+        <citation type="bibtex">
+            @article{McLachlan1999,
+            journal = {Journal of Statistical Software},
+            author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
+            title = {The EMMIX software for the fitting of mixtures of normal and t-components},
+            year = {1999},
+            volume = {4},
+            number = {2},
+            pages = {1-14},}
+        </citation>
+    </citations>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,138 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <token name="@WRAPPER_VERSION@">0.8</token>
+    <xml name="requirements_assembly_post_processor">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_aligner">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_classifier">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_integrator">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_kaks_analysis">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_ks_distribution">
+        <requirements>
+            <requirement type="package" version="1.3.0">r-optparse</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_phylogeny_builder">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </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>
+            <option value="orthofinder">OrthoFinder</option>
+            <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,
+            journal = {None},
+            author = {1. Wafula EK},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {https://github.com/dePamphilis/PlantTribes},}
+        </citation>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/components.tabular	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,7 @@
+species	n	number_comp	lnL	AIC	BIC	mean	variance	porportion
+species1	1160	1	-1404.9900	2813.98	2824.09	0.4426	0.1293	1.00
+species1	1160	2	-1353.6550	2717.31	2742.59	0.7376	0.1672	0.61
+						0.2000	0.0069	0.39
+species1	1160	3	-1323.7480	2663.50	2703.94	0.1214	0.0002	0.10
+						0.7759	0.1663	0.57
+						0.2428	0.0070	0.33
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.pdf	Mon May 01 13:47:20 2017 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rates.tabular	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,101 @@
+SEQ1	SEQ2	Ka	Ks	Ka\Ks
+species1_10079	species1_10080	0.1194	0.9782	0.1221
+species1_10818	species1_10817	0.0194	0.9541	0.0203
+species1_4505	species1_4506	0.0379	0.2411	0.1571
+species1_2890	species1_2889	0.0212	0.8520	0.0249
+species1_3386	species1_3385	0.0002	0.1698	0.0010
+species1_2266	species1_2265	0.0881	0.1515	0.5814
+species1_7052	species1_7051	0.0514	0.8172	0.0630
+species1_3374	species1_3373	0.0034	0.4496	0.0075
+species1_688	species1_687	0.1420	0.2970	0.4782
+species1_10669	species1_10670	0.0003	0.3216	0.0010
+species1_9810	species1_9809	0.1490	0.7782	0.1914
+species1_11440	species1_11439	0.0083	0.2177	0.0380
+species1_2713	species1_2714	0.1227	0.2133	0.5755
+species1_4698	species1_4697	0.1021	0.2207	0.4624
+species1_10939	species1_10940	0.0861	0.7844	0.1098
+species1_22	species1_21	0.1368	0.2515	0.5437
+species1_7149	species1_7150	0.0817	0.9899	0.0825
+species1_5139	species1_5140	0.1167	0.2669	0.4373
+species1_3430	species1_3429	0.0803	0.9931	0.0808
+species1_10208	species1_10207	0.0764	0.1098	0.6957
+species1_8410	species1_8409	0.0165	0.8114	0.0204
+species1_2452	species1_2451	0.0629	0.4523	0.1391
+species1_289	species1_290	0.0560	0.1590	0.3526
+species1_10028	species1_10027	0.0927	1.3078	0.0708
+species1_8242	species1_8241	0.0037	0.1390	0.0264
+species1_5661	species1_5662	0.2040	0.5982	0.3410
+species1_85	species1_86	0.0391	0.1012	0.3866
+species1_1660	species1_1659	0.0408	0.3674	0.1111
+species1_616	species1_615	0.0078	0.1315	0.0595
+species1_8043	species1_8044	0.0637	0.3891	0.1637
+species1_1465	species1_1466	0.1186	0.1725	0.6876
+species1_7761	species1_7762	0.2544	0.3513	0.7242
+species1_299	species1_300	0.1407	0.5325	0.2643
+species1_3563	species1_3564	0.0732	0.1679	0.4360
+species1_4847	species1_4848	0.4327	0.6173	0.7009
+species1_3344	species1_3343	0.0642	0.5842	0.1098
+species1_262	species1_261	0.1786	1.5710	0.1137
+species1_3725	species1_3726	0.1883	0.8863	0.2125
+species1_779	species1_780	0.0725	0.2543	0.2849
+species1_1818	species1_1817	0.0681	0.2312	0.2946
+species1_11023	species1_11024	0.1603	0.6655	0.2408
+species1_9653	species1_9654	0.0007	0.7308	0.0010
+species1_6805	species1_6806	0.1090	0.9048	0.1205
+species1_10221	species1_10222	0.0522	0.1314	0.3975
+species1_6011	species1_6012	0.0099	0.9179	0.0108
+species1_5208	species1_5207	0.0931	0.6077	0.1532
+species1_10692	species1_10691	0.0537	0.1868	0.2876
+species1_10036	species1_10035	0.2450	0.4664	0.5254
+species1_1382	species1_1381	0.0682	0.1241	0.5495
+species1_1350	species1_1349	0.0129	0.4414	0.0293
+species1_6889	species1_6890	0.0195	0.7789	0.0251
+species1_4426	species1_4425	0.0399	0.3048	0.1309
+species1_7405	species1_7406	0.0443	1.3004	0.0341
+species1_11014	species1_11013	0.0643	0.9027	0.0712
+species1_8683	species1_8684	0.1321	0.6680	0.1977
+species1_5287	species1_5288	0.0882	0.3480	0.2534
+species1_11671	species1_11672	0.1101	0.2895	0.3802
+species1_551	species1_552	0.0165	0.2045	0.0809
+species1_3396	species1_3395	0.3309	1.6105	0.2055
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