Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 6:5c7a7484dc51 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:42:48 -0500
parents 945652915244
children dca722aecb67
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5c7a7484dc51 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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1 <tool id="xcms_merge" name="xcms.xcmsSet Merger" version="1.1.0">
0
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2 <description>Merge xcms.xcmsSet xset in one to be used by group</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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8 <expand macro="requirements_light"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 Rscript $script_file
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13 ]]></command>
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15 <configfiles>
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16 <configfile name="script_file"><![CDATA[
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17 suppressPackageStartupMessages(library(xcms, quietly=TRUE))
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19 images=c(
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20 "${"\",\"".join(map(str, $images))}"
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21 )
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24 cat("\tXSET MERGING...\n")
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26 for(image in images) {
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27 load(image)
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28 cat(sampleNamesList\$sampleNamesOrigin,"\n")
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29 if (!exists("xset_merged")) {
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30 xset_merged=xset
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31 singlefile_merged=singlefile
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32 listOFlistArguments_merged=listOFlistArguments
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33 md5sumList_merged=md5sumList
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34 sampleNamesList_merged=sampleNamesList
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35 } else {
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36 xset_merged=c(xset_merged,xset)
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37 singlefile_merged=c(singlefile_merged,singlefile)
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38 listOFlistArguments_merged=c(listOFlistArguments_merged,listOFlistArguments)
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39 md5sumList_merged\$origin=rbind(md5sumList_merged\$origin,md5sumList\$origin)
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40 sampleNamesList_merged\$sampleNamesOrigin=c(sampleNamesList_merged\$sampleNamesOrigin,sampleNamesList\$sampleNamesOrigin)
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41 sampleNamesList_merged\$sampleNamesMakeNames=c(sampleNamesList_merged\$sampleNamesMakeNames,sampleNamesList\$sampleNamesMakeNames)
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42 }
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43 }
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44 rm(image)
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45 xset=xset_merged; rm(xset_merged)
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46 singlefile=singlefile_merged; rm(singlefile_merged)
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47 listOFlistArguments=listOFlistArguments_merged; rm(listOFlistArguments_merged)
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48 md5sumList=md5sumList_merged; rm(md5sumList_merged)
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49 sampleNamesList=sampleNamesList_merged; rm(sampleNamesList_merged)
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51 #if str($sampleMetadata) != 'None':
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52 cat("\tXSET PHENODATA SETTING...\n")
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53 sampleMetadata=read.table("$sampleMetadata", h=F, sep=";", stringsAsFactors=F)
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54 if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep="\t", stringsAsFactors=F)
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55 if (ncol(sampleMetadata) < 2) sampleMetadata=read.table("$sampleMetadata", h=F, sep=",", stringsAsFactors=F)
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56 if (ncol(sampleMetadata) < 2) {
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57 error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
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58 print(error_message)
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59 stop(error_message)
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60 }
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62 sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]
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64 if (any(is.na(sampclass(xset)))) {
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65 sample_missing <- rownames(phenoData(xset))[is.na(sampclass(xset))]
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66 error_message <- paste("Those samples are missing in your sampleMetadata:", paste(sample_missing, collapse=" "))
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67 print(error_message)
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68 stop(error_message)
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69 }
0
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70 #end if
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74 cat("\tXSET OBJECT INFO\n")
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76 print(xset@phenoData)
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77 print(xset)
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79 cat("\tSAVE RData\n")
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80 save.image("$xsetRData")
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82 ]]></configfile>
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83 </configfiles>
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85 <inputs>
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86 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="xset RData / xcms.xcmsSet file" help="output file from another xcms.xcmsSet" multiple="true" />
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87 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
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88 </inputs>
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90 <outputs>
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91 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" />
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92 </outputs>
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94 <tests>
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95 <test>
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96 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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97 <assert_stdout>
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98 <has_text text="object with 4 samples" />
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99 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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100 <has_text text="Mass range: 200.1-600 m/z" />
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101 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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102 <has_text text="Peak Groups: 0" />
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103 <has_text text="Sample classes: ." />
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104 </assert_stdout>
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105 </test>
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106 <test>
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107 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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108 <param name="sampleMetadata" value="sampleMetadata.tab" />
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109 <assert_stdout>
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110 <has_text text="ko15 KO" />
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111 <has_text text="ko16 KO" />
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112 <has_text text="wt15 WT" />
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113 <has_text text="wt16 WT" />
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114 <has_text text="object with 4 samples" />
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115 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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116 <has_text text="Mass range: 200.1-600 m/z" />
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117 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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118 <has_text text="Peak Groups: 0" />
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119 <has_text text="Sample classes: KO, WT" />
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120 </assert_stdout>
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121 </test>
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122 <test>
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123 <param name="images" value="MM8-xset.RData,MM14-xset.RData" />
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124 <assert_stdout>
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125 <has_text text="object with 2 samples" />
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126 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
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127 <has_text text="Mass range: 117.0357-936.7059 m/z" />
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128 <has_text text="Peaks: 236 (about 118 per sample)" />
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129 <has_text text="Peak Groups: 0" />
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130 <has_text text="Sample classes: ." />
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131 </assert_stdout>
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132 </test>
6
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133 <test expect_failure="True">
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134 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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135 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
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136 <expand macro="test_file_load_single"/>
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137 <assert_stderr>
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138 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
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139 </assert_stderr>
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140 </test>
0
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141 </tests>
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142
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143 <help><![CDATA[
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144
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145 @HELP_AUTHORS@
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146
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147 ===================
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148 Xcms.xcmsSet Merger
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149 ===================
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150
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151 -----------
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152 Description
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153 -----------
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154
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155 This tool will allow you to run one xcms.xcmsSet process per sample in parallel and then to merge all RData images in one.
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156 The result is then suitable for xcms.group.
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157
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158 You can provide a sampleMetadata table to attribute phenotypic value to your samples.
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159
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160
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161 -----------------
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162 Workflow position
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163 -----------------
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164
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165 **Upstream tools**
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166
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167 ========================= ================= =================== ==========
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168 Name output file format parameter
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169 ========================= ================= =================== ==========
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170 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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171 ------------------------- ----------------- ------------------- ----------
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172 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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173 ------------------------- ----------------- ------------------- ----------
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174 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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175 ------------------------- ----------------- ------------------- ----------
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176 ... ... ... ...
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177 ========================= ================= =================== ==========
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178
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179
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180 **Downstream tools**
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181
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182 +---------------------------+--------------------+-----------------+
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183 | Name | Output file | Format |
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184 +===========================+====================+=================+
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185 |xcms.group | xset.RData | rdata.xcms.raw |
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186 +---------------------------+--------------------+-----------------+
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187
4
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188 .. image:: xcms_merge_workflow.png
0
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189
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190 -----------
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191 Input files
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192 -----------
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193
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194 +---------------------------+-----------------------+
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195 | Parameter : num + label | Format |
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196 +===========================+=======================+
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197 | 1 : RData file | rdata.xcms.raw |
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198 +---------------------------+-----------------------+
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199 | 2 : RData file | rdata.xcms.raw |
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200 +---------------------------+-----------------------+
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201 | N : RData file | rdata.xcms.raw |
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202 +---------------------------+-----------------------+
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203 | Optional : sampleMetadata | tsv or csv |
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204 +---------------------------+-----------------------+
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205
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206 Example of a sampleMetadata:
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207
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208 +---------------------------+------------+
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209 |HU_neg_028 | bio |
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210 +---------------------------+------------+
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211 |HU_neg_034 | bio |
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212 +---------------------------+------------+
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213 |Blanc04 | blank |
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214 +---------------------------+------------+
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215 |Blanc06 | blank |
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216 +---------------------------+------------+
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217 |Blanc09 | blank |
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218 +---------------------------+------------+
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219
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220 ------------
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221 Output files
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222 ------------
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223
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224 xset.merged.RData: rdata.xcms.raw format
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225
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226 | Rdata file that is necessary in the next step of the workflow "xcms.group".
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227
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228 ---------------------------------------------------
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229
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230 Changelog/News
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231 --------------
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232
6
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233 **Version 1.0.1 - 13/02/2017**
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234
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235 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
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236
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237
0
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238 **Version 1.0.0 - 03/02/2017**
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239
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240 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
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241
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242 ]]></help>
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243
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244 <expand macro="citation" />
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245 </tool>