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1 <tool id="svr0" name="MySort" version="2017.07.24.8">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 Rscript "${script}"
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="script"><![CDATA[
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12 mixture <- read.csv("$input_mixture", header=T, row.names=1)
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13 signature_matrix = read.csv("$input_signature", header=T, row.names=1)
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14
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15 source("$__tool_directory__/svr_without_rmse_corr.r")
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16 source("$__tool_directory__/plot.r")
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17
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18 result <- SVR(signature_matrix, mixture)
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19 clusterplot <- cluster_plot(result)
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20 barplot <- bar_plot(result)
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21
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22 write.csv(result, "$output_result")
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23 png("$output_clusterplot", width=800, height=800)
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24 clusterplot
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25 invisible(dev.off())
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26 png("$output_barplot", width=800, height=800)
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27 barplot
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28 invisible(dev.off())
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29 ]]></configfile>
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30 </configfiles>
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31 <inputs>
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32 <param type="data" name="input_mixture" format="csv" label="Mixture"/>
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33 <param type="data" name="input_signature" format="csv" label="Signature matrix"/>
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34 </inputs>
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35 <outputs>
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36 <data name="output_result" format="csv" label="Result of ${tool.name} on ${on_string}"/>
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37 <data name="output_clusterplot" format="png" label="Cluster-plot of ${tool.name} on ${on_string}"/>
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38 <data name="output_barplot" format="png" label="Bar-plot of ${tool.name} on ${on_string}"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input_mixture" value="mixture.csv"/>
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43 <param name="input_signature" value="signature_matrix.csv"/>
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44 <output name="output_result" file="result.csv"/>
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45 <output name="output_clusterplot" file="clusterplot.png"/>
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46 <output name="output_barplot" file="barplot.png"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50
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51 **What it does**
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52
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53 | MySort is a R program to estimate the fraction and abundance of immune cells based on gene expression profile in heterogeneous mixture tissues.
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54 |
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55 | Citation: MySort - A Gene Profiling Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues.
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56
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57
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58 ----
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59
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60 **Inputs**
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61
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62 .. class:: warningmark
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63
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64 | Comma-separated values (CSV) files ONLY!
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65
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66 * **Mixture file**
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67
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68 | 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.
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69 |
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70
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71 * Example::
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72
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73 17-002 17-006 17-019 17-023 17-026 17-027 17-030 17-034 17-040
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74 7A5 22.31589866 25.28132198 27.09585 22.00866909 28.05138308 19.97328878 23.58830748 22.31589866 24.5900029
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75 A1BG 22.16175149 36.25228433 23.26356028 27.6651914 25.8125363 25.28132198 24.7610399 25.63423608 22.47111801
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76 A1CF 24.25146506 21.25897303 22.31589866 25.45716748 23.75237713 29.24260641 22.47111801 23.91758798 23.58830748
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77 A26C3 22.78480313 23.91758798 21.85664411 30.48441594 24.5900029 25.99207668 19.97328878 27.85761803 23.75237713
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78 A2BP1 42.51794605 22.627417 21.25897303 20.96629446 22.78480313 26.35491255 21.55573723 25.10669113 22.00866909
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79
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80 * **Signature Matrix file**
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81
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82 | 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.
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83 |
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84
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85
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86 * Example::
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87
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88 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)
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89 TCL1A 11762.9329863964 762.792841906926 502.833875600303 117.986529083727 146.531410192506 116.955378976466 69.9673544104057 151.861066666539 117.846466554419 86.5298778848906
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90 ABCB4 564.157988776832 13.2126403514086 9.26333899427403 5.97542505311934 6.31286755665178 9.4956471407396 10.249430943865 8.46885165495616 11.1449931559612 9.09238846544857
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91 AIM2 343.391399738098 4326.07933616138 1381.15051817772 309.918863346619 64.3615794973278 266.515332409956 3191.32538714028 1101.14371410434 397.275565779613 327.315303371804
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92 ZBTB32 12.24039385599 205.845379902139 15.6385731015393 31.3998897051428 33.7819675891862 9.96626463470093 202.575397976579 28.9208257029714 27.0139061691596 77.8965632518407
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93 CD27 402.562878492026 3939.40425295768 6600.97908386608 5292.27278301393 3885.54504835221 4026.06694012145 1110.92273824715 5495.01448261848 1685.96543960432 6725.22726617645
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94
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95 |
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96
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97 ----
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98
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99 **Outputs**
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100
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101 * **Bar plot**
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102
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103 | Bar plot where the x-axis is each experiment and y-axis is the proportion of immune cells.
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104
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105 |
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106
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107 * **Cluster plot**
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108
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109 | Cluster plot shows the hierarchical clustering results of each sample according to the immune cell composition.
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110
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111 |
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112
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113 * **Output file**
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114
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115 | 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.
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116
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117 |
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118
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119 * Example::
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120
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121 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)
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122 17-002 5.86519116086516 5.78172185517755 0 28.0456263712606 0 12.3463700780668 3.70682402906826 2.55582761241995 0 0
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123 17-006 7.96659407050384 0 0 34.3437301458475 0 21.6379512374475 0.410130270925141 6.40140829275814 0 4.06406539184987
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124 17-019 12.1880447552976 4.4170765639818 0 13.6844979546959 0.439003816720928 15.3209721030027 0 0 5.01299153386902 0
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125 17-023 9.29323882302043 4.11131568640441 0 1.61292111594947 0 32.1031844996338 0 2.02029369036927 0 2.03783408522463
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126 17-026 3.64445891248583 8.34951887822622 0 28.1694480957887 0 12.2910782773502 0 3.11105683498932 0 0
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127 17-027 7.14710082306742 8.58148089134017 0 26.1872213672226 4.6902671438807 8.44373238507345 0 3.4328987286918 0 0
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128 17-030 2.11818136872382 8.59539494368935 0 16.3872716875959 0 14.912550920905 0 1.8127028236438 7.58859854878188 0
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129 17-034 7.25696740663024 0 0.543172049350818 4.13758563880151 9.28035161185525 18.7470450023791 0 1.36823975273019 8.49903967754987 0
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130 17-040 11.6655203206611 0 0.328516427461942 10.7770898907558 0 11.8748718361016 4.08443320076682 4.81389646437365 0.994290664613396 0
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131
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132 |
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133
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134 ]]></help>
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135 <citations>
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136 <citation type="bibtex">
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137 </citation>
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138 </citations>
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139 </tool>
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