Mercurial > repos > bgruening > music_manipulate_eset

annotate manipulate_eset.xml @ 4:b5185a4f5209 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 7b4e1e85d9d288a904444eb9fcb96bcdc856b9ff
author bgruening
date Wed, 06 Nov 2024 23:21:49 +0000
parents 22232092be53
children
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22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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1 <tool id="music_manipulate_eset" name="Manipulate Expression Set Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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2 profile="21.09" license="GPL-3.0-or-later" >
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3 <description>Manipulate ExpressionSet objects by a variety of attributes</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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b5185a4f5209 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 7b4e1e85d9d288a904444eb9fcb96bcdc856b9ff
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 cat '$conf' >> /dev/stderr &&
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11 Rscript --vanilla '$conf'
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12
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="conf" >
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16 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
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17 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
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18
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19 vec_ranges = function(vstr) {
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20 ## convert '3:1,22,12:15' to '3,2,1,22,12,13,14,15'
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21 unlist(sapply(unlist(strsplit(vstr, split=",")),
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22 function(x) {
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23 tmp = as.integer(unlist(strsplit(x, split=":")))
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24 if (length(tmp) > 1) {
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25 seq(tmp[[1]], tmp[[2]])
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26 } else {
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27 tmp[[1]]
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28 }
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29 }, USE.NAMES=FALSE))
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30 }
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31
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32 null_str_vec = function(gstr){
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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33 tokens = unlist(as.vector(strsplit(gstr, split=",")))
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34 if (length(tokens) == 0){
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35 return(NULL)
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36 }
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37 if (length(tokens) == 1){
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38 return(tokens[[1]])
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39 }
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40 return(tokens)
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41 }
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42
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43 get_subs = function(values, by_method){
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44 if (by_method == "subsample") {
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45 sample(as.integer(values))
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46 } else if (by_method == "labels") {
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47 null_str_vec(values)
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48 } else if (by_method == "range_and_index") {
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49 vec_ranges(values)
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50 } else {
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51 NA ## equivalent to ALL
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52 }
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53 }
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54
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55 rds_eset = readRDS('$rds_eset')
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56 #if str($combine_eset.do) == "Yes":
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57 new_eset = combine(rds_eset,
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58 #for $e, $egroup in enumerate($combine_eset.eset_group):
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59 readRDS('$egroup.eset')
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60 #if $e != len($combine_eset.eset_group)-1
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61 ,
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62 #end if
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63 #end for
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64 )
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65 #else
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66 new_eset = rds_eset
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67 #end if
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68 sub_eset = new_eset
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69 #if str($subset_eset.do) == "Yes":
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70 #if str($subset_eset.subset_yes.by) == "phenotype":
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71 #for $s, $sgroup in enumerate($subset_eset.subset_yes.pheno_samples)
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72 sub_eset = sub_eset[ ,sub_eset[['$sgroup.column']] %in% c(null_str_vec('$sgroup.values'))]
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73 #end for
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74 #for $g, $ggroup in enumerate($subset_eset.subset_yes.pheno_genes)
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75 sub_eset = sub_eset[sub_eset[['$ggroup.column']] %in% c(null_str_vec('$ggroup.values')), ]
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76 #end for
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77 #else
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78 genes = get_subs('$subset_eset.subset_yes.genes', '$subset_eset.subset_yes.by')
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79 samples = get_subs('$subset_eset.subset_yes.samples', '$subset_eset.subset_yes.by')
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80 sub_eset = sub_eset[genes, samples]
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81 #end if
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82 #end if
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83
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84 ## print data to stdout
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85 print(sub_eset)
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86 saveRDS(sub_eset, file= '$out_eset')
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87
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88 </configfile>
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89 </configfiles>
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90 <inputs>
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91 <param name="rds_eset" label="Expression Set Dataset" type="data" format="@RDATATYPE@" />
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92 <conditional name="combine_eset" >
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93 <param name="do" type="select" label="Concatenate other Expression Set objects?"
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94 help="Phenotype data must match between objects, and objects will be concatenated in the order given below." >
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95 <option value="No" selected="true" >No</option>
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96 <option value="Yes" >Yes</option>
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97 </param>
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98 <when value="No" ></when>
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99 <when value="Yes" >
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100 <repeat name="eset_group" title="Additional Dataset" min="1" >
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101 <param name="eset" label="Expression Set Dataset" type="data" format="@RDATATYPE@" />
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102 </repeat>
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103 </when>
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104 </conditional>
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105 <conditional name="subset_eset" >
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106 <param name="do" type="select" label="Subset the dataset?"
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107 help="If multiple objects are concatenated as in the above section, the resulting object will be subsetted." >
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108 <option value="No" selected="true" >No</option>
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109 <option value="Yes" >Yes</option>
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110 </param>
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111 <when value="No" ></when>
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112 <when value="Yes" >
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113 <conditional name="subset_yes" >
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114 <param name="by" type="select" label="By"
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115 help="e.g. random subsampling, index ranges and indices, specific labels, phenotype conditions" >
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116 <option value="subsample" selected="true" >Random Subsample</option>
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117 <option value="labels" >Specific Labels</option>
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118 <option value="range_and_index" >Index Ranges and Specific Indices</option>
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119 <option value="phenotype" >Filter Samples and Genes by Phenotype Values</option>
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120 </param>
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121 <when value="subsample" >
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122 <param name="samples" type="integer" label="Select N Samples"
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123 value="" optional="true" help="e.g. '10' will select 10 random samples." />
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124 <param name="genes" type="integer" label="Select N Genes"
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125 value="" optional="true" help="e.g. '123' will select 123 random genes." />
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126 </when>
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127 <when value="labels" >
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128 <param name="samples" type="text" label="List of Sample Labels, comma-delimited"
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129 value="" optional="true" help="e.g. 'Control1,ALPOL56,SampleX' would select just those 3 samples." />
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130 <param name="genes" type="text" label="List of Gene Labels , comma-delimited"
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131 value="" optional="true" help="e.g. 'GeneA,GeneX,Gene123' would select just those 3 genes." />
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132 </when>
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133 <when value="range_and_index" >
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134 <param name="samples" type="text"
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135 label="List of Sample Indexes, ranges are colon-delimited, seperated by commas."
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136 value="" optional="true" help="e.g. '5:3,57:60,27' would yield '5,4,3,57,58,59,60,27' " />
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137 <param name="genes" type="text"
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138 label="List of Gene Indexes, ranges are colon-delimited, seperated by commas."
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139 value="" optional="true" help="e.g. '15:18,26,27,3:1' would yield '15,16,17,18,26,27,3,2,1' " />
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140 </when>
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141 <when value="phenotype" >
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142 <repeat name="pheno_samples" title="Filter Samples by Condition" min="0" >
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143 <param name="column" type="text" value="" label="Name of phenotype column"
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144 help="e.g. 'gender' or 'control' etc"/>
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145 <param name="values" type="text" value="" label="List of values in this column to filter for, comma-delimited"
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146 help="e.g. 'female,unknown' selects only samples with values in the above phenotype column of 'female' and 'unknown'."/>
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147 </repeat>
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148 <repeat name="pheno_genes" title="Filter Genes by Condition" min="0" >
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149 <param name="column" type="text" value="" label="Name of phenotype column"
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150 help="e.g. 'housekeeping' or 'marker' etc"/>
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151 <param name="values" type="text" value="" label="List of values in this column to filter for, comma-delimited"
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152 help="e.g. '' selects only samples with values in the above phenotype column of 'female' and 'unknown'."/>
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153 </repeat>
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154 </when>
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155 </conditional>
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156 </when>
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157 </conditional>
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158 </inputs>
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159 <outputs>
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160 <data name="out_eset" format="@RDATATYPE@" label="${tool.name} on ${on_string}: ExpressionSet Object" />
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161 </outputs>
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162 <tests>
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163 <test expect_num_outputs="1" >
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164 <!-- No operation, do nothing -->
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165 <param name="rds_eset" value="Control_Bulk.rds" />
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166 <output name="out_eset" value="Control_Bulk.rds" compare="sim_size" />
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167 </test>
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168 <test expect_num_outputs="1" >
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169 <!-- No concat, subset by ranges -->
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170 <param name="rds_eset" value="Control_Bulk.rds" />
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171 <conditional name="combine_eset" >
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172 <param name="do" value="No" />
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173 </conditional>
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174 <conditional name="subset_eset" >
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175 <param name="do" value="Yes" />
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176 <conditional name="subset_yes" >
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177 <param name="by" value="range_and_index" />
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178 <param name="samples" value="2:3" />
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179 <param name="genes" value="100:20,22,1:5" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
180 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
181 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
182 <assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
183 <has_text text="assayData: 87 features, 2 samples" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
184 </assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
185 </test>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
186 <test expect_num_outputs="1" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
187 <!-- Concat and subset by ranges -->
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
188 <param name="rds_eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
189 <conditional name="combine_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
190 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
191 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
192 <param name="eset" value="APOL1_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
193 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
194 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
195 <param name="eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
196 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
197 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
198 <conditional name="subset_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
199 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
200 <conditional name="subset_yes" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
201 <param name="by" value="range_and_index" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
202 <param name="samples" value="5:7,1" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
203 <param name="genes" value="100:20,22,1:3" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
204 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
205 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
206 <assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
207 <has_text text="assayData: 85 features, 4 samples" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
208 </assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
209 </test>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
210 <test expect_num_outputs="1" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
211 <!-- Concat and subset by labels -->
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
212 <param name="rds_eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
213 <conditional name="combine_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
214 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
215 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
216 <param name="eset" value="APOL1_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
217 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
218 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
219 <conditional name="subset_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
220 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
221 <conditional name="subset_yes" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
222 <param name="by" value="labels" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
223 <param name="samples" value="control.NA.27,control.NA.39" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
224 <param name="genes" value="Nqo1,Card14,Scube2,Nup214" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
225 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
226 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
227 <assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
228 <has_text text="assayData: 4 features, 2 samples" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
229 <has_text text="sampleNames: control.NA.27 control.NA.39" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
230 </assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
231 </test>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
232 <test expect_num_outputs="1" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
233 <!-- Concat and subset by filtering phenotype data -->
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
234 <param name="rds_eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
235 <conditional name="combine_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
236 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
237 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
238 <param name="eset" value="APOL1_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
239 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
240 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
241 <param name="eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
242 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
243 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
244 <conditional name="subset_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
245 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
246 <conditional name="subset_yes" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
247 <param name="by" value="phenotype" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
248 <repeat name="pheno_samples" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
249 <param name="column" value="Control" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
250 <param name="values" value="control" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
251 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
252 <repeat name="pheno_samples" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
253 <param name="column" value="sampleID" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
254 <param name="values" value="3" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
255 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
256 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
257 </conditional>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
258 <assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
259 <has_text text="assayData: 19033 features, 1 samples" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
260 <has_text text="sampleNames: control.NA.39" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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parents:
diff changeset
261 </assert_stdout>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
262 </test>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
263 <test expect_num_outputs="1" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
264 <!-- Concat and random subsample -->
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
265 <param name="rds_eset" value="Control_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
266 <conditional name="combine_eset" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
267 <param name="do" value="Yes" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
268 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
269 <param name="eset" value="APOL1_Bulk.rds" />
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
270 </repeat>
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
bgruening
parents:
diff changeset
271 <repeat name="eset_group" >
22232092be53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit d007ae51743e621dc47524f681501e72ef3a2910"
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272 <param name="eset" value="Control_Bulk.rds" />
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273 </repeat>
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274 </conditional>
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275 <conditional name="subset_eset" >
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276 <param name="do" value="Yes" />
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277 <conditional name="subset_yes" >
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278 <param name="by" value="subsample" />
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279 <param name="samples" value="3" />
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280 <param name="genes" value="25" />
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281 </conditional>
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282 </conditional>
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283 <assert_stdout>
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284 <has_text text="assayData: 25 features, 3 samples" />
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285 </assert_stdout>
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286 </test>
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287 </tests>
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288 <help><![CDATA[
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289 Manipulate an ExpressionSet object by concatenation and or subsetting.
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290
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291 For more options and information, consult `the manual <http://www.bioconductor.org/packages/release/bioc/vignettes/Biobase/inst/doc/ExpressionSetIntroduction.pdf>`_ and the `rdocumentation <https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet>`_
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292 .
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293 ]]></help>
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294 <citations>
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295 <citation type="bibtex">
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296 @misc{falcon2007introduction,
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297 title={An introduction to bioconductor’s expressionset class},
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298 author={Falcon, Seth and Morgan, Martin and Gentleman, Robert},
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299 year={2007}
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300 }
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301 </citation>
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302 </citations>
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303 </tool>