Mercurial > repos > ethevenot > checkformat

annotate checkformat_config.xml @ 1:e194eec8e70c draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
author ethevenot
date Sat, 06 Aug 2016 11:54:28 -0400
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children b6a6b4cc932a
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e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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1 <tool id="checkFormat" name="Check Format" version="2.0.4">
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2 <description>Checks the formats of the dataMatrix, sampleMetadata, and variableMetadata files</description>
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4 <requirements>
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5 <requirement type="package" version="3.2.2">R</requirement>
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6 <requirement type="package">r-batch</requirement>
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7 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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13 <command><![CDATA[
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14 Rscript $__tool_directory__/checkformat_wrapper.R
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15 dataMatrix_in "$dataMatrix_in"
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16 sampleMetadata_in "$sampleMetadata_in"
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17 variableMetadata_in "$variableMetadata_in"
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19 information "$information"
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20 ]]></command>
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22 <inputs>
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23 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
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24 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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25 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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26 </inputs>
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28 <outputs>
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29 <data name="information" label="${tool.name}_information.txt" format="txt"/>
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30 </outputs>
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32 <tests>
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33 <test>
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34 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
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35 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
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36 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
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37 <output name="information" file="output-information.txt" lines_diff="4"/>
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38 </test>
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39 </tests>
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41 <help>
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43 .. class:: infomark
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45 **Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
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47 ---------------------------------------------------
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49 .. class:: infomark
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51 **Tool updates**
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53 See the **NEWS** section at the bottom of this page
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55 ---------------------------------------------------
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57 ========================
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58 Check Format
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59 ========================
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61 -----------
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62 Description
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63 -----------
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65 | Checks the format (row and column names) of the dataMatrix, sampleMetadata and variableMetadata tables
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68 -----------------
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69 Workflow position
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70 -----------------
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72 .. image:: ./static/images/checkFormat_workflowPositionImage.png
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73 :width: 600
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77 -----------
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78 Input files
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79 -----------
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81 +----------------------------+---------+
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82 | Parameter : num + label | Format |
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83 +============================+=========+
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84 | 1 : Data matrix file | tabular |
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85 +----------------------------+---------+
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86 | 2 : Sample metadata file | tabular |
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87 +----------------------------+---------+
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88 | 3 : Variable metadata file | tabular |
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89 +----------------------------+---------+
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91 |
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92 | **Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are**
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93 | **described in the HowTo entitled 'Format Data For Postprocessing' available on the**
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94 | **main page of Workflow4Metabolomics.org**
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95 |
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96
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97 ------------
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98 Output files
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99 ------------
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100
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101 information.txt
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102 | Text file with all messages when error(s) in formats are detected
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103 |
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104
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105 ---------------------------------------------------
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106
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107 ---------------
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108 Working example
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109 ---------------
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110
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111 .. class:: infomark
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112
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113 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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114
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115 ---------------------------------------------------
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116
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117 ----
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118 NEWS
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119 ----
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120
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121 CHANGES IN VERSION 2.0.4
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122 ========================
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123
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124 INTERNAL MODIFICATIONS
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125
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126 Minor internal modifications
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127
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128 CHANGES IN VERSION 2.0.2
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129 ========================
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130
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131 INTERNAL MODIFICATIONS
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132
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133 Test for R code
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134 Planemo running validation
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135 Planemo installing validation
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136 Travis automated testing
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137 Toolshed export
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138
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139 </help>
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140
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141 <citations>
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142 <citation type="bibtex">@Article{Thevenot2015,
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143 Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
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144 Author = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
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145 Journal = {Journal of Proteome Research},
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146 Year = {2015},
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147 Note = {PMID: 26088811},
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148 Number = {8},
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149 Pages = {3322-3335},
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150 Volume = {14},
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151
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152 Doi = {10.1021/acs.jproteome.5b00354},
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153 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
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154 }</citation>
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155 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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156 </citations>
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157
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158
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159
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160 ---------------
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161 Working example
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162 ---------------
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163
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164
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165 Input files
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166 ===========
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167
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168 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
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169 | **1) copy/paste the values below in three distinct .txt files**
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170 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
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171 | **a) File Format: 'tabular'**
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172 | **b) Convert spaces to tabs: 'Yes'**
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173 |
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174
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175 **dataMatrix file**::
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176
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177 dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
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178 HMDB01032 2569204.92420381 6222035.77434915 17070707.9912636 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 4970265.57952158 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
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179 HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 3260583.81592376 8932005.5351622 8340827.52597275 9256460.69197759 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
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180 HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 6030501.02648005 474901.604069803 2885792.42617652 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
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181
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182
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183 **sampleMetadata file**::
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184
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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185 sampleMetadata age ageGrp
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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186 HU_017 41 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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187 HU_021 34 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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188 HU_027 37 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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189 HU_032 38 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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190 HU_041 28 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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191 HU_048 39 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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192 HU_049 50 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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193 HU_050 30 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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194 HU_052 51 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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195 HU_059 81 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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196 HU_060 55 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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197 HU_066 25 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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198 HU_072 47 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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199 HU_077 27 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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200 HU_091 46 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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201 HU_109 32 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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202 HU_110 50 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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203 HU_125 58 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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204 HU_126 45 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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205 HU_131 42 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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206 HU_134 48 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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207 HU_149 35 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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208 HU_150 49 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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209 HU_173 55 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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210 HU_179 33 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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211 HU_180 53 senior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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212 HU_182 43 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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213 HU_202 42 experienced
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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214 HU_204 31 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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215 HU_209 17.5 junior
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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216
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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217
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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218 **variableMetadata file**::
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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219
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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220 variableMetadata name
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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221 HMDB01032 Dehydroepiandrosterone sulfate
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
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222 HMDB03072 Quinic acid
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
ethevenot
parents:
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223 HMDB00792 Sebacic acid
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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224
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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225
e194eec8e70c planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
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226 </tool>