Mercurial > repos > ethevenot > checkformat

annotate checkformat_config.xml @ 0:059eb452931e draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
author ethevenot
date Tue, 24 Oct 2017 08:44:02 -0400
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059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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">r-batch</requirement>
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6 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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12 <command><![CDATA[
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13 Rscript $__tool_directory__/checkformat_wrapper.R
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14 dataMatrix_in "$dataMatrix_in"
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15 sampleMetadata_in "$sampleMetadata_in"
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16 variableMetadata_in "$variableMetadata_in"
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18 information "$information"
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19 ]]></command>
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21 <inputs>
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22 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
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23 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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24 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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25 </inputs>
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27 <outputs>
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28 <data name="information" label="${tool.name}_information.txt" format="txt"/>
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29 </outputs>
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31 <tests>
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32 <test>
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33 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
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34 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
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35 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
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36 <output name="information" file="output-information.txt" lines_diff="4"/>
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37 </test>
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38 </tests>
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40 <help>
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42 .. class:: infomark
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44 **Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
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46 ---------------------------------------------------
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48 .. class:: infomark
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50 **Tool updates**
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52 See the **NEWS** section at the bottom of this page
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54 ---------------------------------------------------
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56 ========================
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57 Check Format
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58 ========================
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60 -----------
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61 Description
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62 -----------
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63
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64 | Checks the format (row and column names) of the dataMatrix, sampleMetadata and variableMetadata tables
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65
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66
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67 -----------------
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68 Workflow position
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69 -----------------
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71 .. image:: ./static/images/checkFormat_workflowPositionImage.png
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72 :width: 600
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76 -----------
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77 Input files
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78 -----------
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80 +----------------------------+---------+
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81 | Parameter : num + label | Format |
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82 +============================+=========+
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83 | 1 : Data matrix file | tabular |
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84 +----------------------------+---------+
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85 | 2 : Sample metadata file | tabular |
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86 +----------------------------+---------+
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87 | 3 : Variable metadata file | tabular |
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88 +----------------------------+---------+
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90 |
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91 | **Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are**
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92 | **described in the HowTo entitled 'Format Data For Postprocessing' available on the**
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93 | **main page of Workflow4Metabolomics.org**
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94 |
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96 ------------
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97 Output files
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98 ------------
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100 information.txt
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101 | Text file with all messages when error(s) in formats are detected
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102 |
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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 Working example
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108 ---------------
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109
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110 .. class:: infomark
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111
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112 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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113
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114 ---------------------------------------------------
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115
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116 ----
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117 NEWS
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118 ----
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119
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120 CHANGES IN VERSION 2.0.4
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121 ========================
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122
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123 INTERNAL MODIFICATIONS
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124
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125 Minor internal modifications
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126
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127 CHANGES IN VERSION 2.0.2
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128 ========================
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129
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130 INTERNAL MODIFICATIONS
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131
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132 Test for R code
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133 Planemo running validation
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134 Planemo installing validation
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135 Travis automated testing
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136 Toolshed export
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137
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138 </help>
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139
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140 <citations>
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141 <citation type="bibtex">@Article{Thevenot2015,
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142 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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143 Author = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe},
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144 Journal = {Journal of Proteome Research},
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145 Year = {2015},
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146 Note = {PMID: 26088811},
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147 Number = {8},
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148 Pages = {3322-3335},
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149 Volume = {14},
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150
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151 Doi = {10.1021/acs.jproteome.5b00354},
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152 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
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153 }</citation>
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154 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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155 </citations>
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156 <!--
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157
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158
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159 Working example
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160
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161
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162
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163 Input files
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164 ===========
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165
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166 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
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167 | **1) copy/paste the values below in three distinct .txt files**
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168 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
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169 | **a) File Format: 'tabular'**
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170 | **b) Convert spaces to tabs: 'Yes'**
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171 |
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172
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173 **dataMatrix file**::
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174
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175 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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176 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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177 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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178 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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179
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180
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181 **sampleMetadata file**::
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182
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183 sampleMetadata age ageGrp
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184 HU_017 41 experienced
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185 HU_021 34 junior
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186 HU_027 37 experienced
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187 HU_032 38 experienced
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188 HU_041 28 junior
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189 HU_048 39 experienced
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190 HU_049 50 senior
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191 HU_050 30 junior
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192 HU_052 51 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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193 HU_059 81 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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194 HU_060 55 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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195 HU_066 25 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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196 HU_072 47 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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197 HU_077 27 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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198 HU_091 46 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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199 HU_109 32 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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200 HU_110 50 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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201 HU_125 58 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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202 HU_126 45 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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203 HU_131 42 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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204 HU_134 48 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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205 HU_149 35 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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206 HU_150 49 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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207 HU_173 55 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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208 HU_179 33 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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209 HU_180 53 senior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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210 HU_182 43 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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211 HU_202 42 experienced
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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212 HU_204 31 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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213 HU_209 17.5 junior
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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214
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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215
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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216 **variableMetadata file**::
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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217
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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218 variableMetadata name
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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219 HMDB01032 Dehydroepiandrosterone sulfate
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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220 HMDB03072 Quinic acid
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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221 HMDB00792 Sebacic acid
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
ethevenot
parents:
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222 -->
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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223
059eb452931e planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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224 </tool>