comparison nusvm.xml @ 0:e3afe097e80a draft default tip

First commit

0:e3afe097e80a

<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>