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1 <tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.0">
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2 <description>data in ascending or descending order</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
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8 </expand>
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9 <version_command>sort --version | head -n 1</version_command>
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10 <command>
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11 <![CDATA[
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12 (
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13 #if int($header) > 0:
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14 sed -u '${header}'q &&
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15 #end if
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16
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17 sort $unique $ignore_case --stable -t ' '
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18
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19 #for $key in $sortkeys:
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20 -k '${key.column}${key.order}${key.style},${key.column}'
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21 #end for
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22
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23 ) < '${infile}' > '${outfile}'
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param format="tabular" name="infile" type="data" label="Sort Query" />
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28 <param name="header" type="integer" size="5" value="0"
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29 label="Number of header lines" help="These will be ignored during sort.">
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30 <validator type="in_range" message="Negative values are not allowed." min="0"/>
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31 </param>
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32
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33 <repeat name="sortkeys" title="Column selections" min="1">
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34 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
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35 <param name="order" type="select" display="radio" label="in">
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36 <option value="">Ascending order</option>
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37 <option value="r">Descending order</option>
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38 </param>
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39 <param name="style" type="select" display="radio" label="Flavor">
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40 <option value="n">Fast numeric sort (-n)</option>
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41 <option value="g">General numeric sort ( scientific notation -g)</option>
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42 <option value="V">Natural/Version sort (-V) </option>
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43 <option value="">Alphabetical sort</option>
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44 <option value="h">Human-readable numbers (-h)</option>
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45 <option value="R">Random order (-R)</option>
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46 </param>
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47 </repeat>
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48
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49 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
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50 label="Output unique values" help="Print only unique values, based on sorted key columns. See help section for details. (--unique)" />
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51 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue=""
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52 label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters. (-i)" />
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53
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54 </inputs>
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55 <outputs>
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56 <data format="input" name="outfile" metadata_source="infile"/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="infile" value="sort_in1.bed"/>
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61 <param name="header" value="3"/>
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62 <repeat name="sortkeys">
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63 <param name="column" value="1"/>
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64 <param name="style" value=""/>
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65 <param name="order" value=""/>
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66 </repeat>
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67 <repeat name="sortkeys">
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68 <param name="column" value="3"/>
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69 <param name="style" value="n"/>
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70 <param name="order" value="r"/>
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71 </repeat>
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72 <output name="outfile" file="sort_result1.bed"/>
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73 </test>
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74 <test>
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75 <param name="infile" value="sort_in1.bed"/>
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76 <param name="header" value="3"/>
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77 <repeat name="sortkeys">
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78 <param name="column" value="1"/>
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79 <param name="style" value=""/>
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80 <param name="order" value=""/>
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81 </repeat>
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82 <repeat name="sortkeys">
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83 <param name="column" value="3"/>
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84 <param name="style" value="n"/>
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85 <param name="order" value=""/>
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86 </repeat>
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87 <output name="outfile" file="sort_result2.bed"/>
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88 </test>
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89 <test>
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90 <param name="infile" value="sort_in2.bed"/>
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91 <repeat name="sortkeys">
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92 <param name="column" value="5"/>
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93 <param name="style" value="g"/>
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94 <param name="order" value=""/>
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95 </repeat>
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96 <output name="outfile" file="sort_result3.bed"/>
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97 </test>
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98 </tests>
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99 <help>
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100 <![CDATA[
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101 **What it does**
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102
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103 This tool sorts an input file.
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104
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105 -----
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106
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107 **Sorting Styles**
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108
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109 * **Fast Numeric**: sort by numeric values. Handles integer values (e.g. 43, 134) and decimal-point values (e.g. 3.14). *Does not* handle scientific notation (e.g. -2.32e2).
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110 * **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary.
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111 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
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112 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
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113 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
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114 * **Random order**: return lines in random order.
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115
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116 ------
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117
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118 **Example - Header line**
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119
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120 **Input file** (note first line is a header line, should not be sorted)::
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121
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122 Fruit Color Price
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123 Banana Yellow 4.1
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124 Avocado Green 8.0
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125 Apple Red 3.0
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126 Melon Green 6.1
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127
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128 **Sorting** by **numeric order** on column **3**, with **header**, will return::
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129
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130 Fruit Color Price
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131 Apple Red 3.0
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132 Banana Yellow 4.1
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133 Melon Green 6.1
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134 Avocado Green 8.0
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135
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136
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137 -----
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138
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139 **Example - Natural vs. Alphabetical sorting**
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140
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141 Given the following list::
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142
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143 chr4
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144 chr13
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145 chr1
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146 chr10
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147 chr20
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148 chr2
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149
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150 **Alphabetical sort** would produce the following sorted list::
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151
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152 chr1
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153 chr10
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154 chr13
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155 chr2
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156 chr20
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157 chr4
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158
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159 **Natural Sort** would produce the following sorted list::
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160
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161 chr1
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162 chr2
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163 chr4
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164 chr10
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165 chr13
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166 chr20
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167
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168
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169 .. class:: infomark
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170
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171 If you're planning to use the file with another tool that expected sorted files (such as *join*), you should use the **Alphabetical sort**, not the **Natural Sort**. Natural sort order is easier for humans, but is unnatural for computer programs.
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172
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173 @REFERENCES@
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174 ]]>
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175 </help>
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176 </tool>
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