diff nusvm.xml @ 0:e3afe097e80a draft default tip

First commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nusvm.xml	Thu Jul 27 22:24:59 2017 -0400
@@ -0,0 +1,139 @@
+<tool id="svr0" name="MySort" version="2017.07.24.8">
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        Rscript "${script}"
+    ]]></command>
+    <configfiles>
+        <configfile name="script"><![CDATA[
+mixture <- read.csv("$input_mixture", header=T, row.names=1)
+signature_matrix = read.csv("$input_signature", header=T, row.names=1)
+
+source("$__tool_directory__/svr_without_rmse_corr.r")
+source("$__tool_directory__/plot.r")
+
+result <- SVR(signature_matrix, mixture)
+clusterplot <- cluster_plot(result)
+barplot <- bar_plot(result)
+
+write.csv(result, "$output_result")
+png("$output_clusterplot", width=800, height=800) 
+clusterplot
+invisible(dev.off())
+png("$output_barplot", width=800, height=800) 
+barplot
+invisible(dev.off())
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+	<param type="data" name="input_mixture" format="csv" label="Mixture"/>
+        <param type="data" name="input_signature" format="csv" label="Signature matrix"/>
+    </inputs>
+    <outputs>
+        <data name="output_result" format="csv" label="Result of ${tool.name} on ${on_string}"/>
+        <data name="output_clusterplot" format="png" label="Cluster-plot of ${tool.name} on ${on_string}"/>
+        <data name="output_barplot" format="png" label="Bar-plot of ${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_mixture" value="mixture.csv"/>
+            <param name="input_signature" value="signature_matrix.csv"/>
+            <output name="output_result" file="result.csv"/>
+            <output name="output_clusterplot" file="clusterplot.png"/>
+            <output name="output_barplot" file="barplot.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+ | MySort is a R program to estimate the fraction and abundance of immune cells based on gene expression profile in heterogeneous mixture tissues.
+ |
+ | Citation: MySort - A Gene Profiling Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues.
+
+
+----
+
+**Inputs**
+
+  .. class:: warningmark
+
+  | Comma-separated values (CSV) files ONLY!
+
+* **Mixture file**
+
+  | Mixture file contains the gene expression profiles of samples. Each column refers to different experimental conditions. Each row represents the expression level of the gene symbol.
+  |
+
+* Example::
+
+	 	17-002		17-006		17-019		17-023		17-026		17-027		17-030		17-034		17-040
+	7A5	22.31589866	25.28132198	27.09585	22.00866909	28.05138308	19.97328878	23.58830748	22.31589866	24.5900029
+	A1BG	22.16175149	36.25228433	23.26356028	27.6651914	25.8125363	25.28132198	24.7610399	25.63423608	22.47111801
+	A1CF	24.25146506	21.25897303	22.31589866	25.45716748	23.75237713	29.24260641	22.47111801	23.91758798	23.58830748
+	A26C3	22.78480313	23.91758798	21.85664411	30.48441594	24.5900029	25.99207668	19.97328878	27.85761803	23.75237713
+	A2BP1	42.51794605	22.627417	21.25897303	20.96629446	22.78480313	26.35491255	21.55573723	25.10669113	22.00866909
+
+* **Signature Matrix file**
+
+  | Signature matrix file is the gene expression signature profiles of each cell type. Each column refers to a single immune cell type. Each row represents the expression value of selected signature genes, which are used to estimate the abundance of immune cells.
+  |
+
+
+* Example::
+
+		B cells naive		B cells memory		Plasma cells		T cells CD8		T cells CD4 naive	T cells CD4 memory resting	T cells CD4 memory activated	T cells follicular helper	T cells gamma delta	T cells regulatory (Tregs)
+	TCL1A	11762.9329863964	762.792841906926	502.833875600303	117.986529083727	146.531410192506	116.955378976466		69.9673544104057		151.861066666539		117.846466554419	86.5298778848906
+	ABCB4	564.157988776832	13.2126403514086	9.26333899427403	5.97542505311934	6.31286755665178	9.4956471407396			10.249430943865			8.46885165495616		11.1449931559612	9.09238846544857
+	AIM2	343.391399738098	4326.07933616138	1381.15051817772	309.918863346619	64.3615794973278	266.515332409956		3191.32538714028		1101.14371410434		397.275565779613	327.315303371804
+	ZBTB32	12.24039385599		205.845379902139	15.6385731015393	31.3998897051428	33.7819675891862	9.96626463470093		202.575397976579		28.9208257029714		27.0139061691596	77.8965632518407
+	CD27	402.562878492026	3939.40425295768	6600.97908386608	5292.27278301393	3885.54504835221	4026.06694012145		1110.92273824715		5495.01448261848		1685.96543960432	6725.22726617645
+
+  |
+
+----
+
+**Outputs**
+
+* **Bar plot**
+
+  | Bar plot where the x-axis is each experiment and y-axis is the proportion of immune cells.
+  
+  |
+
+* **Cluster plot**
+
+  | Cluster plot shows the hierarchical clustering results of each sample according to the immune cell composition.
+
+  |
+
+* **Output file**
+
+  | Output file is the immune cell proportions of each experiment. Each column refers to a single immune cell type. Each row represents different experimental conditions.
+
+  |
+
+* Example::
+
+		B cells naive           B cells memory          Plasma cells            T cells CD8             T cells CD4 naive       T cells CD4 memory resting      T cells CD4 memory activated    T cells follicular helper       T cells gamma delta     T cells regulatory (Tregs)
+	17-002	5.86519116086516	5.78172185517755	0			28.0456263712606	0			12.3463700780668		3.70682402906826		2.55582761241995		0			0
+	17-006	7.96659407050384	0			0			34.3437301458475	0			21.6379512374475		0.410130270925141		6.40140829275814		0			4.06406539184987
+	17-019	12.1880447552976	4.4170765639818		0			13.6844979546959	0.439003816720928	15.3209721030027		0				0				5.01299153386902	0	
+	17-023	9.29323882302043	4.11131568640441	0			1.61292111594947	0			32.1031844996338		0				2.02029369036927		0			2.03783408522463
+	17-026	3.64445891248583	8.34951887822622	0			28.1694480957887	0			12.2910782773502		0				3.11105683498932		0			0
+	17-027	7.14710082306742	8.58148089134017	0			26.1872213672226	4.6902671438807		8.44373238507345		0				3.4328987286918			0			0
+	17-030	2.11818136872382	8.59539494368935	0			16.3872716875959	0			14.912550920905			0				1.8127028236438			7.58859854878188	0
+	17-034	7.25696740663024	0			0.543172049350818	4.13758563880151	9.28035161185525	18.7470450023791		0				1.36823975273019		8.49903967754987	0
+	17-040	11.6655203206611	0			0.328516427461942	10.7770898907558	0			11.8748718361016		4.08443320076682		4.81389646437365		0.994290664613396	0	
+
+  |
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+        </citation>
+    </citations>
+</tool>