Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 5:a4d1b79479a5 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:46:43 -0400
parents 945652915244
children 5c7a7484dc51
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1 <tool id="xcms_merge" name="xcms.xcmsSet Merger" version="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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3
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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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50
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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("$sampleMetadata", h=F, sep=",", stringsAsFactors=F)
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56 if (ncol(sampleMetadata) < 2) {
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57 error_message="Your sampleMetadata file seems not well formatted. The column separators accepted are ; , and tabulation"
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58 print(error_message)
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59 stop(error_message)
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60 }
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61
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62 sampclass(xset)=sampleMetadata\$V2[match(rownames(xset@phenoData),sampleMetadata\$V1)]
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63 #end if
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67 cat("\tXSET OBJECT INFO\n")
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68
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69 print(xset@phenoData)
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70 print(xset)
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72 cat("\tSAVE RData\n")
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73 save.image("$xsetRData")
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74
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75 ]]></configfile>
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76 </configfiles>
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78 <inputs>
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79 <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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80 <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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81 </inputs>
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82
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83 <outputs>
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84 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" />
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85 </outputs>
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86
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87 <tests>
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88 <test>
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89 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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90 <assert_stdout>
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91 <has_text text="object with 4 samples" />
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92 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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93 <has_text text="Mass range: 200.1-600 m/z" />
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94 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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95 <has_text text="Peak Groups: 0" />
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96 <has_text text="Sample classes: ." />
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97 </assert_stdout>
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98 </test>
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99 <test>
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100 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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101 <param name="sampleMetadata" value="sampleMetadata.tab" />
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102 <assert_stdout>
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103 <has_text text="ko15 KO" />
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104 <has_text text="ko16 KO" />
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105 <has_text text="wt15 WT" />
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106 <has_text text="wt16 WT" />
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107 <has_text text="object with 4 samples" />
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108 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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109 <has_text text="Mass range: 200.1-600 m/z" />
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110 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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111 <has_text text="Peak Groups: 0" />
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112 <has_text text="Sample classes: KO, WT" />
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113 </assert_stdout>
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114 </test>
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115 <test>
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116 <param name="images" value="MM8-xset.RData,MM14-xset.RData" />
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117 <assert_stdout>
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118 <has_text text="object with 2 samples" />
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119 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
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120 <has_text text="Mass range: 117.0357-936.7059 m/z" />
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121 <has_text text="Peaks: 236 (about 118 per sample)" />
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122 <has_text text="Peak Groups: 0" />
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123 <has_text text="Sample classes: ." />
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124 </assert_stdout>
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125 </test>
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126 </tests>
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127
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128 <help><![CDATA[
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129
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130 @HELP_AUTHORS@
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131
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132 ===================
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133 Xcms.xcmsSet Merger
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134 ===================
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135
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136 -----------
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137 Description
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138 -----------
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139
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140 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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141 The result is then suitable for xcms.group.
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142
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143 You can provide a sampleMetadata table to attribute phenotypic value to your samples.
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144
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145
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146 -----------------
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147 Workflow position
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148 -----------------
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149
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150 **Upstream tools**
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151
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152 ========================= ================= =================== ==========
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153 Name output file format parameter
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154 ========================= ================= =================== ==========
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155 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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156 ------------------------- ----------------- ------------------- ----------
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157 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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158 ------------------------- ----------------- ------------------- ----------
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159 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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160 ------------------------- ----------------- ------------------- ----------
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161 ... ... ... ...
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162 ========================= ================= =================== ==========
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163
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164
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165 **Downstream tools**
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166
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167 +---------------------------+--------------------+-----------------+
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168 | Name | Output file | Format |
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169 +===========================+====================+=================+
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170 |xcms.group | xset.RData | rdata.xcms.raw |
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171 +---------------------------+--------------------+-----------------+
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172
4
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173 .. image:: xcms_merge_workflow.png
0
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174
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175 -----------
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176 Input files
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177 -----------
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178
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179 +---------------------------+-----------------------+
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180 | Parameter : num + label | Format |
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181 +===========================+=======================+
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182 | 1 : RData file | rdata.xcms.raw |
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183 +---------------------------+-----------------------+
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184 | 2 : RData file | rdata.xcms.raw |
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185 +---------------------------+-----------------------+
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186 | N : RData file | rdata.xcms.raw |
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187 +---------------------------+-----------------------+
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188 | Optional : sampleMetadata | tsv or csv |
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189 +---------------------------+-----------------------+
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190
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191 Example of a sampleMetadata:
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192
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193 +---------------------------+------------+
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194 |HU_neg_028 | bio |
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195 +---------------------------+------------+
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196 |HU_neg_034 | bio |
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197 +---------------------------+------------+
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198 |Blanc04 | blank |
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199 +---------------------------+------------+
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200 |Blanc06 | blank |
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201 +---------------------------+------------+
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202 |Blanc09 | blank |
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203 +---------------------------+------------+
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204
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205 ------------
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206 Output files
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207 ------------
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208
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209 xset.merged.RData: rdata.xcms.raw format
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210
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211 | Rdata file that is necessary in the next step of the workflow "xcms.group".
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212
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213 ---------------------------------------------------
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214
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215 Changelog/News
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216 --------------
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217
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218 **Version 1.0.0 - 03/02/2017**
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219
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220 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
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221
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222 ]]></help>
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223
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224 <expand macro="citation" />
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225 </tool>