Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 3:f439ed7a8f03 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:09:25 -0400
parents 3a5204f14fff
children a26679f68d4d
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1 <tool id="xcms_merge" name="xcms findChromPeaks Merger" version="@WRAPPER_VERSION@.0">
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2 <description>Merge xcms findChromPeaks RData into a unique file 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 <import>macros_xcms.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/xcms_merge.r
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15 images 'c("${"\",\"".join(map(str, $images))}")'
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17 #if str($sampleMetadata) != 'None':
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18 sampleMetadata '$sampleMetadata'
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19 #end if
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21 @COMMAND_FILE_LOAD@
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22 ]]></command>
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24 <inputs>
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25 <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
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26 <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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27
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28 <expand macro="input_file_load"/>
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29 </inputs>
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31 <outputs>
3
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32 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="xset.merged.RData" from_work_dir="merged.RData" />
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33 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
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34 <filter>not sampleMetadata</filter>
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35 </data>
0
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36 </outputs>
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38 <tests>
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39 <!-- DISABLE FOR TRAVIS
0
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40 <test>
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41 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
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42 <expand macro="test_file_load_single"/>
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43 <assert_stdout>
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44 <has_text text="object with 4 samples" />
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45 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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46 <has_text text="Mass range: 200.1-600 m/z" />
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47 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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48 <has_text text="Peak Groups: 0" />
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49 <has_text text="Sample classes: ." />
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50 </assert_stdout>
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51 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
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52 </test>
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53 -->
0
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54 <test>
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55 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
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56 <expand macro="test_file_load_single"/>
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57 <param name="sampleMetadata" value="sampleMetadata.tab" />
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58 <assert_stdout>
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59 <has_text_matching expression="ko15\s+KO" />
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60 <has_text_matching expression="ko16\s+KO" />
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61 <has_text_matching expression="wt15\s+WT" />
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62 <has_text_matching expression="wt16\s+WT" />
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63 <has_text text="object with 4 samples" />
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64 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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65 <has_text text="Mass range: 200.1-600 m/z" />
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66 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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67 <has_text text="Peak Groups: 0" />
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68 <has_text text="Sample classes: KO, WT" />
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69 </assert_stdout>
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70 </test>
3
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71 <!--<test expect_failure="True">
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72 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
2
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73 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
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74 <expand macro="test_file_load_single"/>
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75 <assert_stderr>
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76 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
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77 </assert_stderr>
3
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78 </test>-->
0
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79 </tests>
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81 <help><![CDATA[
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82
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83 @HELP_AUTHORS@
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84
3
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85 ==========================
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86 xcms findChromPeaks Merger
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87 ==========================
0
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89 -----------
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90 Description
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91 -----------
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92
3
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93 This tool allows you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images into one.
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94 The result is then suitable for xcms groupChromPeaks.
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95
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96 You can provide a sampleMetadata table to attribute phenotypic values to your samples.
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97
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98
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99 -----------------
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100 Workflow position
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101 -----------------
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102
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103 **Upstream tools**
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104
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105 ========================= ===================== ==============================
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106 Name Output file Format
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107 ========================= ===================== ==============================
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108 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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109 ------------------------- --------------------- ------------------------------
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110 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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111 ------------------------- --------------------- ------------------------------
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112 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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113 ------------------------- --------------------- ------------------------------
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114 ... ... ...
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115 ------------------------- --------------------- ------------------------------
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116 Upload file [optional] sampleMetadata tabular
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117 ========================= ===================== ==============================
0
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118
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119
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120 **Downstream tools**
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121
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122 =========================== ==================== ============================
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123 Name Output file Format
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124 =========================== ==================== ============================
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125 xcms.groupChromPeaks xset.merged.RData rdata.xcms.findchrompeaks
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126 =========================== ==================== ============================
0
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127
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128 .. image:: xcms_merge_workflow.png
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129
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130 -----------
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131 Input files
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132 -----------
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133
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134 =========================== ==================================
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135 Parameter : num + label Format
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136 =========================== ==================================
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137 1 : RData file rdata.xcms.findchrompeaks
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138 --------------------------- ----------------------------------
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139 2 : RData file rdata.xcms.findchrompeaks
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140 --------------------------- ----------------------------------
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141 N : RData file rdata.xcms.findchrompeaks
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142 --------------------------- ----------------------------------
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143 Optional : sampleMetadata tsv or csv
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144 =========================== ==================================
0
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145
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146 Example of a sampleMetadata:
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147
3
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148 =========================== ============
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149 Samples class
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150 =========================== ============
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151 HU_neg_028 bio
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152 --------------------------- ------------
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153 HU_neg_034 bio
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154 --------------------------- ------------
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155 Blanc04 blank
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156 --------------------------- ------------
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157 Blanc06 blank
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158 --------------------------- ------------
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159 Blanc09 blank
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160 =========================== ============
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161
0
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162
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163 ------------
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164 Output files
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165 ------------
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166
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167 xset.merged.RData: rdata.xcms.findchrompeaks format
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168
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169 | Rdata file that is necessary in the next step of the workflow "xcms.groupChromPeaks".
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170
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171 ---------------------------------------------------
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172
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173 Changelog/News
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174 --------------
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175
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176 **Version 3.0.0.0 - 08/03/2018**
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177
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178 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
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179
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180 - IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data.
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181
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182 - IMPROVMENT: the tool will now generate a sampleMetadata file if any was provided. It will be useful to add some further information for the normalization and statistics steps.
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183
2
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184 **Version 1.0.1 - 13/02/2017**
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185
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186 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
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187
0
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188 **Version 1.0.0 - 03/02/2017**
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189
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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190 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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191
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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192 ]]></help>
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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193
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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194 <expand macro="citation" />
47f9b1fd5ce6 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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195 </tool>