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1 <tool id="pathprint-fingerprint" name="Create Pathway Fingerprint">
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2
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3 <!--
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4 <description>Create Pathway Fingerprint.</description>
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5 -->
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6
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7 <command>
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8 fingerprint.r
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9 #if $query.type == "geo"
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10 geo $query.input $output
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11 #elif $query.type == "cel"
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12 cel $query.input $output
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13 #elif $query.type == "expr"
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14 expr $query.input $query.platform $output
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15 #end if
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16 <!--
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17 > /dev/null 2>&1
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18 -->
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19 </command>
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20
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21 <inputs>
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22 <conditional name="query">
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23 <param name="type" type="select" label="Query source" help="Select an expression matrix from your User History, or enter a GEO identifier to automatically download an experiment from GEO.">
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24 <option value="geo">GEO ID</option>
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25 <!-- <option value="cel">CEL File</option> -->
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26 <option value="expr" selected="true">Expression Matrix</option>
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27 </param>
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28
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29 <when value="geo">
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30 <param name="input" size="10" type="text" value="GSM99618" label="GEO ID" help="GSM and GSE identifiers are supported. E.g. GSM99618 or GSE4416. Please see below for the list of supported platforms.">
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31 <validator type="regex" message="The provided GEO ID does not appear to be valid.">^(GSM|GSE|gsm|gse)\d+$</validator>
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32 </param>
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33 </when>
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34
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35 <!-- shs 042412: no affycel file type available in Upload File -->
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36 <!-- <when value="cel">
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37 <param name="input" type="data" label="CEL file" help="Submit an Affymetrix CEL file from your history"/>
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38 </when> -->
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39
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40 <when value="expr">
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41 <param name="input" type="data" label="Expression Matrix" help="The expression matrix is required to have the following format: columns = samples; rows = normalized expression values." />
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42
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43 <param name="platform" type="select" label="Platform" help="Select the array platform. Only those in the dropdown list are supported.">
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44 <option value="GPL72">GPL72 - Affymetrix Drosophila Genome Array</option>
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45 <option value="GPL81">GPL81 - Affymetrix Mouse Genome U74A Version 2 Array</option>
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46 <option value="GPL85">GPL85 - Affymetrix Rat Genome U34 Array</option>
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47 <option value="GPL91">GPL91 - Affymetrix Human Genome U95A Array</option>
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48 <option value="GPL96">GPL96 - Affymetrix Human Genome U133A Array</option>
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49 <option value="GPL200">GPL200 - Affymetrix C. elegans Genome Array</option>
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50 <option value="GPL339">GPL339 - Affymetrix Mouse Expression 430A Array</option>
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51 <option value="GPL341">GPL341 - Affymetrix Rat Expression 230A Array</option>
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52 <option value="GPL570">GPL570 - Affymetrix Human Genome U133 Plus 2.0 Array</option>
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53 <option value="GPL571">GPL571 - Affymetrix Human Genome U133A 2.0 Array</option>
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54 <option value="GPL1261">GPL1261 - Affymetrix Mouse Genome 430 2.0 Array</option>
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55 <option value="GPL1319">GPL1319 - Affymetrix Zebrafish Genome Array</option>
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56 <option value="GPL1322">GPL1322 - Affymetrix Drosophila Genome 2.0 Array</option>
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57 <option value="GPL1355">GPL1355 - Affymetrix Rat Genome 230 2.0 Array</option>
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58 <option value="GPL2700">GPL2700 - Sentrix HumanRef-8 Expression BeadChip</option>
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59 <option value="GPL2986">GPL2986 - ABI Human Genome Survey Microarray Version 2</option>
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60 <option value="GPL2995">GPL2995 - ABI Mouse Genome Survey Microarray</option>
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61 <option value="GPL3921">GPL3921 - Affymetrix HT Human Genome U133A Array</option>
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62 <option value="GPL4685">GPL4685 - Affymetrix GeneChip HT-HG_U133A Early Access Array</option>
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63 <option value="GPL6102">GPL6102 - Illumina human-6 v2.0 expression beadchip</option>
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64 <option value="GPL6103">GPL6103 - Illumina mouseRef-8 v1.1 expression beadchip</option>
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65 <option value="GPL6104">GPL6104 - Illumina humanRef-8 v2.0 expression beadchip</option>
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66 <option value="GPL6105">GPL6105 - Illumina mouse-6 v1.1 expression beadchip</option>
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67 <option value="GPL6244">GPL6244 - Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]</option>
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68 <option value="GPL6246">GPL6246 - Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]</option>
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69 <option value="GPL6333">GPL6333 - Illumina Mouse Ref-6 V1</option>
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70 <option value="GPL6883">GPL6883 - Illumina HumanRef-8 v3.0 expression beadchip</option>
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71 <option value="GPL6884">GPL6884 - Illumina HumanWG-6 v3.0 expression beadchip</option>
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72 <option value="GPL6885">GPL6885 - Illumina MouseRef-8 v2.0 expression beadchip</option>
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73 <option value="GPL6887">GPL6887 - Illumina MouseWG-6 v2.0 expression beadchip</option>
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74 <option value="GPL6947">GPL6947 - Illumina HumanHT-12 v3.0 expression beadchip</option>
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75 <option value="GPL8300">GPL8300 - Affymetrix Human Genome U95 Version 2 Array</option>
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76 <option value="GPL8321">GPL8321 - Affymetrix Mouse Genome 430A 2.0 Array</option>
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77 </param>
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78 </when>
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79 </conditional>
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80 </inputs>
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81
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82 <outputs>
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83 <data format="tabular" name="output" label="PathPrint fingerprint"/>
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84 </outputs>
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85
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86 <stdio>
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87 <exit_code range="1:" level="fatal" />
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88 </stdio>
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89
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90 <help>
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91
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92 **What it does**
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93
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94 This tool computes a functional pathway profile for the input data. Gene expression values
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95 for each sample are mapped to a set of 633 pathways that have been curated from KEGG,
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96 Reactome, WikiPathways and Netpath. Pathways are assigned a value of [-1,0,1], where -1
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97 indicates low expression, 0 indicates average expression, and +1 indicates high expression
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98 of the pathway relative to a background comprised of 188,502 arrays from the Gene
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99 Expression Omnibus (GEO).
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100
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101 .. class:: infomark
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102
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103 Be sure to select the appropriate platform for your experiment or you may get spurious results. A list of supported platforms is available at the http://compbio.sph.harvard.edu/hidelab/pathprint/Platform_coverage.html.
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104
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105 -----
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106
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107 **Input**
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108
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109 1. Expression Matrix (tabular format): columns represent samples and rows are normalized expression values for each sample. Also specify the appropriate platform (see note above).
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110
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111 OR
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112
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113 2. GEO series ID (GSE) or sample ID (GSM)
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114
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115
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116 **Output**
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117
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118 PathPrint Fingerprint: a tabular format file where columns represent samples and
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119 row values are pathway activities
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120
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121 -----
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122
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123 Feedback is welcome. Please send your questions, comments and suggestions to scde@hsci.harvard.edu.
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124 </help>
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125 </tool>
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126
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