Mercurial > repos > ethevenot > checkformat

annotate checkformat_config.xml @ 4:9590fac86f63 draft

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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 46e92656192f2714265cc525b283c7cbb87b9093
author ethevenot
date Wed, 28 Feb 2018 05:47:44 -0500
parents 80a38d36f946
children
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1 <tool id="checkFormat" name="Check Format" version="3.0.0">
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2 <description>Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files</description>
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4 <requirements>
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5 <requirement type="package" version="1.1_4">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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17 makeNameL "$makeNameL"
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19 dataMatrix_out "$dataMatrix_out"
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20 sampleMetadata_out "$sampleMetadata_out"
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21 variableMetadata_out "$variableMetadata_out"
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22 information "$information"
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23 ]]></command>
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25 <inputs>
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26 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
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27 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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28 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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29 <param name="makeNameL" label="Make syntactically valid sample and variable names" type="select" help="">
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30 <option value="TRUE">yes</option>
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31 <option value="FALSE" selected="true">no</option>
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32 </param>
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33 </inputs>
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35 <outputs>
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36 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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37 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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38 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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39 <data name="information" label="${tool.name}_information.txt" format="txt"/>
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40 </outputs>
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42 <tests>
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43 <test>
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44 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
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45 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
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46 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
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47 <param name="makeNameL" value="TRUE"/>
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48 <output name="information">
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49 <assert_contents>
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50 <has_text text="Message: Converting sample and variable names to the standard R format" />
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51 <has_text text="Warning: The sample and/or variable names or orders from the input tables have been modified" />
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56
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57 <help><![CDATA[
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59 .. class:: infomark
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61 **Author** Etienne Thevenot (W4M Core Development Team, MetaboHUB Paris, CEA)
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63 ---------------------------------------------------
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65 .. class:: infomark
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67 **Tool updates**
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69 See the **NEWS** section at the bottom of this page
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71 ---------------------------------------------------
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72
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73 ============
1
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74 Check Format
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75 ============
1
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77 -----------
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78 Description
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79 -----------
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80
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81 | **Checks the format (row and column names)** of the dataMatrix, sampleMetadata and variableMetadata tables; in case of difference of orders of the samples and/or variables between (some of) the tables, the **orders from the dataMatrix are permuted** to match those of the sampleMetadata and/or the variableMetadata; sample and variables names can also be modified to be **syntactically valid** for R by selecting the corresponding argument (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.).
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84 -----------------
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85 Workflow position
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86 -----------------
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88 .. image:: ./static/images/checkFormat_workflowPositionImage.png
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89
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91 -----------
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92 Input files
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93 -----------
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94
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95 +----------------------------+---------+
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96 | Parameter : num + label | Format |
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97 +============================+=========+
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98 | 1 : Data matrix file | tabular |
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99 +----------------------------+---------+
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100 | 2 : Sample metadata file | tabular |
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101 +----------------------------+---------+
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102 | 3 : Variable metadata file | tabular |
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103 +----------------------------+---------+
3
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104
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105 | The **required formats** for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org (http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf)
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106
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107
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108 ----------
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109 Parameters
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110 ----------
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111
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112 Data matrix file
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113 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
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114 |
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115
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116 Sample metadata file
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117 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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118 |
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119
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120 Variable metadata file
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121 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
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122 |
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123
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124 Make syntactically valid sample and variable names
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125 | if set to 'yes', sample and variable names will converted to syntactically valid names with the 'make.names' R function when required (e.g. an 'X' is added to names starting with a digit, blanks will be converted to '.', etc.)
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126 |
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127
1
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128 ------------
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129 Output files
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130 ------------
3
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131
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132 dataMatrix_out.tabular
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133 | dataMatrix data file; may be identical to the input dataMatrix in case no renaming of sample/variable names nor re-ordering of samples/variables (see the 'information' file for the presence/absence of modifications)
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134 |
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135
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136 sampleMetadata_out.tabular
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137 | sampleMetadata data file; may be identical to the input sampleMetadata in case no renaming of sample names nor re-ordering of samples (see the 'information' file for the presence/absence of modifications)
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138 |
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139
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140 variableMetadata_out.tabular
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141 | variableMetadata data file; may be identical to the input variableMetadata in case no renaming of variable names nor re-ordering of variables (see the 'information' file for the presence/absence of modifications)
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142 |
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143
1
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144 information.txt
3
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145 | Text file with all messages when error(s) in formats are detected
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146 |
1
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147
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148 ---------------------------------------------------
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149
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150 ---------------
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151 Working example
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152 ---------------
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153
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154 .. class:: infomark
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155
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156 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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157
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158 ---------------------------------------------------
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159
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160 ----
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161 NEWS
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162 ----
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163
3
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164 CHANGES IN VERSION 3.0.0
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165 ========================
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166
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167 NEW FEATURES
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168
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169 Automated re-ordering (if necessary) of sample and/or variable names from dataMatrix based on sampleMetadata and variableMetadata
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170
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171 New argument to make sample and variable names syntactically valid
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172
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173 Output of dataMatrix, sampleMetadata, and variableMetadata files, whether they have been modified or not
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174
1
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175 CHANGES IN VERSION 2.0.4
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176 ========================
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177
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178 INTERNAL MODIFICATIONS
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179
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180 Minor internal modifications
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181
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182 CHANGES IN VERSION 2.0.2
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183 ========================
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184
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185 INTERNAL MODIFICATIONS
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186
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187 Test for R code
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188 Planemo running validation
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189 Planemo installing validation
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190 Travis automated testing
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191 Toolshed export
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192
3
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193 ]]></help>
1
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194
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195 <citations>
3
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196 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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197 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
1
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198 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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199 </citations>
3
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200
1
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201
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202 </tool>