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annotate datamash.xml @ 10:ee35019e3cba

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merged updates to 1.0.6 from test-toolshed
author Assaf Gordon <agordon@wi.mit.edu>
date Sat, 22 Nov 2014 21:13:52 -0500
parents f6af66d4ded6
children
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f6af66d4ded6 Datamash: update Galaxy Tool ID
Assaf Gordon <assafgordon@gmail.com>
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1 <tool id="Datamash" name="Datamash" version="1.0.5">
0
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2 <description>(operations on tabular data)</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.0.5">datamash</requirement>
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6 </requirements>
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7
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8 <command>
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9 datamash
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10 $header_in
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11 $header_out
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12 $need_sort
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13 $print_full_line
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14 $ignore_case
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15 #if str($grouping)>0
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16 --group '$grouping'
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17 #end if
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18 #for $oper in $operations
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19 ${oper.op_name}
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20 ${oper.op_column}
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21 #end for
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22 &lt; $in_file &gt; $out_file
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23 </command>
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24 <inputs>
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25 <param format="tabular" name="in_file" type="data" label="Select Input Data" help=""/>
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26
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27 <param name="grouping" label="Group by fields" type="text" help="Example: 1,4 - To group by the first and fourth fields. Leave empty to perform operation on entire file as one group."/>
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28
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29 <param name="header_in" type="boolean" truevalue="--header-in" falsevalue=""
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30 label="Input file has a header line" help="Mark this if the input file's first line is a header line" />
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31
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32 <param name="header_out" type="boolean" truevalue="--header-out" falsevalue=""
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33 label="Print header line" help="Mark this if you want the first line to show the field names" />
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34
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35 <param name="need_sort" type="boolean" truevalue="--sort" falsevalue=""
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36 label="Sort input" help="Mark if the input file is not sorted. If the input file is already sorted, unmark this option to reduce computing time." />
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37
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38 <param name="print_full_line" type="boolean" truevalue="--full" falsevalue=""
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39 label="Print all fields from input file" help="If set, all input fields will be printed. If unset, only fields used for grouping will be printed." />
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40
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41 <param name="ignore_case" type="boolean" truevalue="--ignore-case" falsevalue=""
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42 label="Ignore case when grouping" help="If set, upper/lowercase differences will be ignored when grouping fields." />
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43
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44 <repeat name="operations" title="Operation to perform on each group">
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45 <param name="op_name" type="select" label="Type">
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46 <option value="count">count</option>
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47 <option value="sum">sum</option>
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48 <option value="min">minimum</option>
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49 <option value="max">maximum</option>
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50 <option value="absmin">Absolute minimum</option>
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51 <option value="absmax">Absolute maximum</option>
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52 <option value="mean">Mean</option>
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53 <option value="pstdev">Population Standard deviantion</option>
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54 <option value="sstdev">Sample Standard deviantion</option>
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55 <option value="median">Median</option>
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56 <option value="q1">1st quartile</option>
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57 <option value="q3">3rd quartile</option>
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58 <option value="iqr">Inter-quartile range</option>
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59 <option value="mad">Median Absolute Deviation</option>
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60 <option value="pvar">Variance (population)</option>
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61 <option value="svar">Variance (sample)</option>
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62 <option value="sskew">Skewness (sample)</option>
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63 <option value="pskew">Skewness (population)</option>
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64 <option value="skurt">Kurtosis (sample)</option>
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65 <option value="pkurt">Kurtosis (population)</option>
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66 <option value="jarque">Jarque-Bera Normality test</option>
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67 <option value="dpo">DAgostino-Pearson Omnibus Normality Test</option>
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68 <option value="mode">Mode</option>
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69 <option value="antimode">Anti-Mode</option>
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70 <option value="unique">Combine all unique values</option>
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71 <option value="collapse">Combine all values</option>
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72 <option value="countunique">Count Unique values</option>
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73 </param>
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74 <param name="op_column" label="On column" type="data_column" data_ref="in_file" />
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75 </repeat>
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76 </inputs>
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77
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78 <outputs>
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79 <data format="tabular" name="out_file" />
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80 </outputs>
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81
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82 <tests>
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83 <test>
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84 <param name="in_file" value="group_compute_input.txt" />
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85 <param name="grouping" value="2" />
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86 <param name="header_in" value="true" />
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87 <param name="header_out" value="true" />
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88 <param name="need_sort" value="true" />
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89 <param name="print_full_line" value="false" />
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90 <param name="op_column" value="3" />
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91 <param name="op_name" value="sum" />
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92 <param name="ignore_case" value="false" />
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93 <output name="out_file" file="group_compute_output.txt" />
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94 </test>
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95 </tests>
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96 <help>
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97
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98 .. class:: infomark
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99
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100 **TIP:** Input data must be TAB delimited. If the desired dataset does not appear in the input list, use *Text Manipulation-&gt;Convert* to convert it to **Tabular** type.
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101
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102 -----
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103
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104 **Syntax**
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105
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106 This tools performs common operations (such as summing, counting, mean, standard-deviation) on input file, based on tabular data. The tool can also optionaly group the input based on a given field.
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107
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108 -----
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109
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110 **Example 1**
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111
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112 - Find the average score in statistics course of college students, grouped by their college major. The input file has three fields (Name,Major,Score) and a header line::
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113
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114 Name Major Score
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115 Bryan Arts 68
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116 Isaiah Arts 80
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117 Gabriel Health-Medicine 100
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118 Tysza Business 92
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119 Zackery Engineering 54
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120 ...
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121 ...
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122
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123 - Grouping the input by the second column (*Major*), and performing operations **mean** and **sample standard deviation** on the third column (*Score*), gives::
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124
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125 GroupBy(Major) mean(Score) sstdev(Score)
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126 Arts 68.9474 10.4215
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127 Business 87.3636 5.18214
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128 Engineering 66.5385 19.8814
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129 Health-Medicine 90.6154 9.22441
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130 Life-Sciences 55.3333 20.606
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131 Social-Sciences 60.2667 17.2273
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132
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133 This sample file is available at http://www.gnu.org/software/datamash .
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134
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135 **Example 2**
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136
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137 - Using the UCSC RefSeq Human Gene Track, available at: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
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138
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139 - List the number and identifiers of isoforms per gene. The gene identifier is in column 13, the isoform/transcript identifier is in column 2. Grouping by column 13 and performing **count** and **Combine all values** on column 2, gives::
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140
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141 GroupBy(field-13) count(field-2) collapse(field-2)
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142 A1BG 1 NM_130786
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143 A1BG-AS1 1 NR_015380
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144 A1CF 6 NM_001198818,NM_001198819,NM_001198820,NM_014576,NM_138932,NM_138933
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145 A2M 1 NM_000014
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146 A2M-AS1 1 NR_026971
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147 A2ML1 2 NM_001282424,NM_144670
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148 ...
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149
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150 - Count how many transcripts are listed for each chromosome and strand. Chromosome is on column 3, Strand is in column 4. Transcript identifiers are in column 2. Grouping by columns **3,4** and performing operation **count** on column 2, gives::
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151
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152 GroupBy(field-3) GroupBy(field-4) count(field-2)
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153 chr1 + 2456
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154 chr1 - 2431
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155 chr2 + 1599
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156 chr2 - 1419
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157 chr3 + 1287
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158 chr3 - 1249
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159 ...
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160
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161 -----
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162
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163 **GNU Datamash** is a Free and Open Source Software, see more details on the Datamash_ Website.
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164
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165 **GNU Datamash** is also available as a command-line program, see http://www.gnu.org/software/datamash/download/ .
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166
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167 For more details about supported statistical operations, see Datamash_ website.
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168
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169 .. _Datamash: http://www.gnu.org/software/datamash/
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170
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171 </help>
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172 </tool>