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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/edger_with_design_matrix commit eb5cd7834861d8ddbffce974ed0ca6f1c0ecccf2
author erasmus-medical-center
date Tue, 14 Feb 2017 10:01:51 -0500
parents 55f4e42f91ba
children
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a">
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3 <description>Create design- from an expression matrix</description>
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5 <macros>
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6 <import>edgeR_macros.xml</import>
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7 </macros>
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9 <requirements>
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10 <requirement type="package" version="2.7">python</requirement>
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11 </requirements>
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12
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13 <command>
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14 python '${__tool_directory__}/bin/design_matrix_creator'
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15 -c $expression_matrix
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17 #set $unique_columns = []
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18 #for $factor in $treatments:
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19 #for $level in $factor.rep_factorLevel:
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20 #for $val in $level.factorIndex.value:
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21 #if str($val) not in $unique_columns:
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22 #set $unique_columns = $unique_columns + [str($val)]
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23 #end if
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24 #end for
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25 #end for
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26 #end for
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28 #set $unique_columns = " ".join(unique_columns)
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29 -s $unique_columns
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31 -t
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32 #for $factor in $treatments:
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33 #set $factor_str = str($factor.name).encode('base64').replace('\n','')
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35 #for $level in $factor.rep_factorLevel:
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36 #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value])
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37 #end for
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39 $factor_str
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40 #end for
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42 #if $choose_blocking.choice == "true"
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43 -b
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44 #for blocking in $choose_blocking.blocking_repeat:
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45 #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','')
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47 #for $block_iter in $blocking.block:
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48 #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value])
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49 #set $blocking_str = $blocking_str+":"+$block_str
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50 #end for
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52 $blocking_str
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53 #end for
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54 #end if
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56 -o $design_matrix
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57 </command>
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58
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59 <inputs>
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60 <param name="expression_matrix" format="tabular" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" />
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61
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62 <repeat name="treatments" title="Factor/Condition" min="1">
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63 <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" />
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64 <repeat name="rep_factorLevel" title="Factor level" min="1">
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65 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" />
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66 <param name="factorIndex" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" multiple="true">
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67 <validator type="no_options" message="Please select at least one column." />
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68 </param>
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69 </repeat>
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70 </repeat>
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71
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72 <conditional name="choose_blocking">
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73 <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" >
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74 <option value="false">No</option>
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75 <option value="true">Yes</option>
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76 </param>
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77 <when value="false" />
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78 <when value="true">
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79 <repeat name="blocking_repeat" title="Blocking condition" min="1">
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80 <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" />
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81 <repeat name="block" title="Block" min="2">
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82 <param name="block_index" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" numerical="True" multiple="true" use_header_names="true">
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83 <validator type="no_options" message="Please select at least one column." />
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84 </param>
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85 </repeat>
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86 </repeat>
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87 </when>
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88 </conditional>
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89 </inputs>
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90
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91 <outputs>
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92 <data format="tabular" name="design_matrix" label="Design matrix" />
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93 </outputs>
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94
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95 <tests>
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96 <test>
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97 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
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98
8
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99 <repeat name="treatments">
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100 <repeat name="rep_factorLevel">
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101 <param name="factorLevel" value="Control" />
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102 <param name="factorIndex" value="2,3,4,5,6,7,8" />
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103 </repeat>
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104 <repeat name="rep_factorLevel">
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105 <param name="factorLevel" value="E2" />
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106 <param name="factorIndex" value="9,10,11,12,13,14,15" />
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107 </repeat>
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108 </repeat>
1
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109
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110 <conditional name="choose_blocking">
8
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111 <param name="choice" value="false" />
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112 </conditional>
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113
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114 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" />
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115 </test>
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116 </tests>
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117
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118 <help>
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119 edgeR: Design- from Expression matrix
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120 #####################################
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121
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122 Overview
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123 --------
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124
2
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125 Create a design matrix by selecting the desired patients from an expression matrix.
1
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126
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127 Input
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128 -----
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129
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130 @CONTACT@
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131 </help>
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132
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133 <expand macro="citations" />
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134 </tool>