Mercurial > repos > lecorguille > xcms_merge

annotate xcms_merge.xml @ 10:47e953d9da82 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
author lecorguille
date Thu, 08 Mar 2018 05:52:52 -0500
parents 6b5504f877ff
children 67ab853b89f3
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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 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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7
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @COMMAND_XCMS_SCRIPT@/xcms_merge.r
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13
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14 images 'c("${"\",\"".join(map(str, $images))}")'
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16 #if str($sampleMetadata) != 'None':
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17 sampleMetadata '$sampleMetadata'
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18 #end if
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19
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20 @COMMAND_FILE_LOAD@
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21 ]]></command>
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23 <inputs>
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24 <param name="images" type="data" format="rdata.xcms.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
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25 <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 <expand macro="input_file_load"/>
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28 </inputs>
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30 <outputs>
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31 <data name="xsetRData" format="rdata.xcms.raw" label="xset.merged.RData" from_work_dir="merged.RData" />
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32 <data name="sampleMetadataOutput" format="tabular" label="xset.merged.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv">
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33 <filter>not sampleMetadata</filter>
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34 </data>
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35 </outputs>
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37 <tests>
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38 <!-- DISABLE FOR TRAVIS
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39 <test>
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40 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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41 <expand macro="test_file_load_single"/>
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42 <assert_stdout>
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43 <has_text text="object with 4 samples" />
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44 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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45 <has_text text="Mass range: 200.1-600 m/z" />
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46 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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47 <has_text text="Peak Groups: 0" />
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48 <has_text text="Sample classes: ." />
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49 </assert_stdout>
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50 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
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51 </test>
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52 -->
0
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53 <test>
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54 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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55 <expand macro="test_file_load_single"/>
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56 <param name="sampleMetadata" value="sampleMetadata.tab" />
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57 <assert_stdout>
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58 <has_text_matching expression="ko15\s+KO" />
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59 <has_text_matching expression="ko16\s+KO" />
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60 <has_text_matching expression="wt15\s+WT" />
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61 <has_text_matching expression="wt16\s+WT" />
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62 <has_text text="object with 4 samples" />
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63 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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64 <has_text text="Mass range: 200.1-600 m/z" />
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65 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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66 <has_text text="Peak Groups: 0" />
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67 <has_text text="Sample classes: KO, WT" />
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68 </assert_stdout>
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69 </test>
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70 <!--<test expect_failure="True">
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71 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" />
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72 <param name="sampleMetadata" value="sampleMetadata_missing.tab" />
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73 <expand macro="test_file_load_single"/>
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74 <assert_stderr>
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75 <has_text text="Those samples are missing in your sampleMetadata: ko16" />
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76 </assert_stderr>
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77 </test>-->
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78 </tests>
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80 <help><![CDATA[
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82 @HELP_AUTHORS@
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83
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84 ==========================
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85 xcms findChromPeaks Merger
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86 ==========================
0
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88 -----------
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89 Description
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90 -----------
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91
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92 This tool will allow you to run one xcms findChromPeaks process per sample in parallel and then to merge all RData images in one.
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93 The result is then suitable for xcms groupChromPeaks.
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94
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95 You can provide a sampleMetadata table to attribute phenotypic value to your samples.
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96
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97
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98 -----------------
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99 Workflow position
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100 -----------------
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101
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102 **Upstream tools**
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103
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104 ========================= ================= =================== ==========
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105 Name output file format parameter
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106 ========================= ================= =================== ==========
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107 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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108 ------------------------- ----------------- ------------------- ----------
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109 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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110 ------------------------- ----------------- ------------------- ----------
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111 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
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112 ------------------------- ----------------- ------------------- ----------
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113 ... ... ... ...
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114 ========================= ================= =================== ==========
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115
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116
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117 **Downstream tools**
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118
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119 +---------------------------+--------------------+-----------------+
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120 | Name | Output file | Format |
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121 +===========================+====================+=================+
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122 |xcms.group | xset.RData | rdata.xcms.raw |
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123 +---------------------------+--------------------+-----------------+
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124
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125 .. image:: xcms_merge_workflow.png
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126
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127 -----------
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128 Input files
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129 -----------
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130
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131 +---------------------------+-----------------------+
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132 | Parameter : num + label | Format |
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133 +===========================+=======================+
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134 | 1 : RData file | rdata.xcms.raw |
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135 +---------------------------+-----------------------+
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136 | 2 : RData file | rdata.xcms.raw |
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137 +---------------------------+-----------------------+
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138 | N : RData file | rdata.xcms.raw |
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139 +---------------------------+-----------------------+
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140 | Optional : sampleMetadata | tsv or csv |
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141 +---------------------------+-----------------------+
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142
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143 Example of a sampleMetadata:
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144
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145 +---------------------------+------------+
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146 |HU_neg_028 | bio |
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147 +---------------------------+------------+
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148 |HU_neg_034 | bio |
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149 +---------------------------+------------+
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150 |Blanc04 | blank |
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151 +---------------------------+------------+
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152 |Blanc06 | blank |
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153 +---------------------------+------------+
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154 |Blanc09 | blank |
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155 +---------------------------+------------+
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156
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157 ------------
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158 Output files
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159 ------------
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160
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161 xset.merged.RData: rdata.xcms.raw format
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162
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163 | Rdata file that is necessary in the next step of the workflow "xcms.group".
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164
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165 ---------------------------------------------------
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166
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167 Changelog/News
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168 --------------
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169
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170 **Version 3.0.0.0 - 08/03/2018**
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171
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172 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
6
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173
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174 - IMPROVMENT: a new dedicated tool "xcms plot chromatogram" will allow you to get TIC and BPI of your raw data.
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175
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176 - 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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177
8
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178 **Version 1.0.1 - 13/02/2017**
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179
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180 - IMPROVMENT: the tool will now raise an error if a sample isn't describe in the sampleMetadata file
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181
0
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182 **Version 1.0.0 - 03/02/2017**
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183
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184 - NEW: a new tool to merge individual xcmsSet outputs to be used by xcms.group
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185
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186 ]]></help>
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187
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188 <expand macro="citation" />
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189 </tool>