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annotate sort.xml @ 25:ab83aa685821 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
author bgruening
date Sat, 17 Jan 2026 00:57:38 +0000
parents c41d78ae5fee
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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12615d397df7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f
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1 <tool id="tp_sort_header_tool" name="Sort" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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="creator"/>
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7 <expand macro="requirements">
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ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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8 <requirement type="package" version="4.9">sed</requirement>
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9 </expand>
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10 <version_command>sort --version | head -n 1</version_command>
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11 <command>
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12 <![CDATA[
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13 (
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14 export LC_ALL=C;
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15 #if int($header) > 0:
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16 sed -u '${header}'q &&
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17 #end if
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18
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19 sort $unique --stable -t ' '
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20
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21 #for $key in $sortkeys:
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22 #if $key.start_charpos and $key.end_charpos:
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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23 -k ${key.column}.${key.start_charpos}${key.ignore_leading_blanks},${key.column}.${key.end_charpos}${key.ignore_leading_blanks}${key.order}${key.style}${key.ignore_case}
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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24 #elif $key.start_charpos:
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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25 -k ${key.column}.${key.start_charpos}${key.ignore_leading_blanks},${key.column}${key.order}${key.style}${key.ignore_case}
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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26 #elif $key.end_charpos:
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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27 -k ${key.column}${key.ignore_leading_blanks},${key.column}.${key.end_charpos}${key.ignore_leading_blanks}${key.order}${key.style}${key.ignore_case}
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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28 #else:
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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29 -k ${key.column}${key.ignore_leading_blanks},${key.column}${key.order}${key.style}${key.ignore_case}
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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30 #end if
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31 #end for
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32
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33 ) < '${infile}' > '${outfile}'
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param format="tabular" name="infile" type="data" label="Sort Query" />
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38 <param name="header" type="integer" value="0"
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39 label="Number of header lines" help="Header lines will be copied to the output unchanged without operating on them.">
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40 <validator type="in_range" message="Negative values are not allowed." min="0"/>
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41 </param>
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42
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43 <repeat name="sortkeys" title="Column selections" min="1">
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44 <param name="column" label="Sort on column" type="data_column" data_ref="infile" accept_default="true" />
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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45 <param name="start_charpos" label="considering its characters from" type="integer" min="1" optional="true" help="Leave empty (or set to 1) to use the column value starting from its first character." />
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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46 <param name="end_charpos" label="to and including" type="integer" min="1" optional="true" help="Leave empty to use the column value up to and including its last character." />
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47 <param name="order" type="select" display="radio" label="in">
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48 <option value="">Ascending order</option>
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49 <option value="r">Descending order</option>
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50 </param>
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51 <param name="style" type="select" display="radio" label="using sort flavor">
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52 <option value="n">Fast numeric sort (-n)</option>
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53 <option value="g">General numeric sort ( scientific notation -g)</option>
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54 <option value="V">Natural/Version sort (-V) </option>
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55 <option value="">Alphabetical sort</option>
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56 <option value="h">Human-readable numbers (-h)</option>
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57 <option value="R">Random order (-R)</option>
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58 </param>
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59 <param name="ignore_case" type="boolean" checked="false" truevalue="f" falsevalue=""
ab83aa685821 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 28d2fcf2649b999762fbd94bd648485b916f2f0d
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60 label="ignoring case" help="Turn lowercase symbols to upper case before comparing values in this column. (-f)" />
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61 <param name="ignore_leading_blanks" type="boolean" checked="false" truevalue="b" falsevalue=""
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62 label="ignoring leading blanks" help="This option can be useful with Alphabetical and Natural sort (which treat spaces as actual characters) or to prevent unwanted offsets if you specified a range of character positions to consider." />
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63 </repeat>
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64
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65 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue=""
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66 label="Output unique values" help="Print only unique values, based on sorted key columns. See help section for details. (--unique)" />
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67 </inputs>
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68 <outputs>
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69 <data name="outfile" format_source="infile" metadata_source="infile"/>
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70 </outputs>
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71 <tests>
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72 <test expect_num_outputs="1">
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73 <param name="infile" value="sort1.bed"/>
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74 <param name="header" value="3"/>
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75 <repeat name="sortkeys">
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76 <param name="column" value="1"/>
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77 <param name="style" value=""/>
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78 <param name="order" value=""/>
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79 </repeat>
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80 <repeat name="sortkeys">
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81 <param name="column" value="3"/>
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82 <param name="style" value="n"/>
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83 <param name="order" value="r"/>
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84 </repeat>
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85 <output name="outfile" file="sort_result1.bed"/>
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86 </test>
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87 <test expect_num_outputs="1">
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88 <param name="infile" value="sort1.bed"/>
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89 <param name="header" value="3"/>
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90 <repeat name="sortkeys">
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91 <param name="column" value="1"/>
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92 <param name="style" value=""/>
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93 <param name="order" value=""/>
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94 </repeat>
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95 <repeat name="sortkeys">
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96 <param name="column" value="3"/>
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97 <param name="style" value="n"/>
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98 <param name="order" value=""/>
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99 </repeat>
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100 <output name="outfile" file="sort_result2.bed"/>
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101 </test>
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102 <test expect_num_outputs="1">
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103 <param name="infile" value="sort2.bed"/>
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104 <repeat name="sortkeys">
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105 <param name="column" value="5"/>
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106 <param name="style" value="g"/>
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107 <param name="order" value=""/>
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108 </repeat>
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109 <output name="outfile" file="sort_result3.bed"/>
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110 </test>
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111 <test expect_num_outputs="1">
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112 <param name="infile" value="sort3.tabular"/>
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113 <param name="header" value="0"/>
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114 <param name="unique" value="false"/>
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115 <repeat name="sortkeys">
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116 <param name="column" value="2"/>
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117 <param name="start_charpos" value="7"/>
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118 <param name="order" value=""/>
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119 <param name="style" value="n"/>
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120 </repeat>
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121 <repeat name="sortkeys">
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122 <param name="column" value="2"/>
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123 <param name="start_charpos" value="4"/>
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124 <param name="end_charpos" value="5"/>
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125 <param name="order" value=""/>
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126 <param name="style" value="n"/>
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127 </repeat>
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128 <repeat name="sortkeys">
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129 <param name="column" value="2"/>
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130 <param name="start_charpos" value="1"/>
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131 <param name="end_charpos" value="2"/>
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132 <param name="order" value="r"/>
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133 <param name="style" value="n"/>
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134 </repeat>
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135 <output name="outfile" file="sorted3.tabular" ftype="tabular" />
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136 </test>
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137 <!-- Test ignore_case param -->
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138 <test expect_num_outputs="1">
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139 <param name="infile" value="sort4.tabular"/>
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140 <param name="header" value="1"/>
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141 <param name="unique" value="false"/>
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142 <repeat name="sortkeys">
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143 <param name="column" value="1"/>
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144 <param name="order" value=""/>
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145 <param name="style" value=""/>
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146 <param name="ignore_case" value="true"/>
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147 </repeat>
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148 <repeat name="sortkeys">
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149 <param name="column" value="3"/>
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150 <param name="order" value="r"/>
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151 <param name="style" value="n"/>
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152 </repeat>
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153 <output name="outfile" file="sorted4_partial.tabular" ftype="tabular" />
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154 </test>
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155 <!-- Test ignore_leading_blanks param -->
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156 <test expect_num_outputs="1">
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157 <param name="infile" value="sort4.tabular"/>
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158 <param name="header" value="1"/>
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159 <param name="unique" value="false"/>
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160 <repeat name="sortkeys">
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161 <param name="column" value="1"/>
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162 <param name="start_charpos" value="1"/>
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163 <param name="end_charpos" value="4"/>
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164 <param name="order" value=""/>
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165 <param name="style" value=""/>
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166 <param name="ignore_case" value="true"/>
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167 <param name="ignore_leading_blanks" value="true"/>
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168 </repeat>
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169 <repeat name="sortkeys">
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170 <param name="column" value="1"/>
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171 <param name="start_charpos" value="5"/>
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172 <param name="order" value=""/>
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173 <param name="style" value=""/>
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174 <param name="ignore_case" value="true"/>
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175 <param name="ignore_leading_blanks" value="true"/>
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176 </repeat>
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177 <repeat name="sortkeys">
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178 <param name="column" value="3"/>
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179 <param name="order" value="r"/>
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180 <param name="style" value="n"/>
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181 <param name="ignore_leading_blanks" value="true"/>
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182 </repeat>
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183 <output name="outfile" file="sorted4.tabular" ftype="tabular" />
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184 </test>
0
5314e5d6f040 Imported from capsule None
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185 </tests>
5314e5d6f040 Imported from capsule None
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186 <help>
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187 <![CDATA[
5314e5d6f040 Imported from capsule None
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188 **What it does**
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189
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190 This tool sorts an input file.
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191
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192 -----
5314e5d6f040 Imported from capsule None
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193
5314e5d6f040 Imported from capsule None
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194 **Sorting Styles**
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195
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196 * **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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197 * **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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198 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below.
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199 * **Alphabetical sort**: Sort in strict alphabetical order. See example below.
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200 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400)
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201 * **Random order**: return lines in random order.
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202
5314e5d6f040 Imported from capsule None
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203 ------
5314e5d6f040 Imported from capsule None
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204
5314e5d6f040 Imported from capsule None
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205 **Example - Header line**
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206
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207 **Input file** (note first line is a header line, should not be sorted)::
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208
5314e5d6f040 Imported from capsule None
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209 Fruit Color Price
5314e5d6f040 Imported from capsule None
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210 Banana Yellow 4.1
5314e5d6f040 Imported from capsule None
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211 Avocado Green 8.0
5314e5d6f040 Imported from capsule None
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212 Apple Red 3.0
5314e5d6f040 Imported from capsule None
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213 Melon Green 6.1
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214
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215 **Sorting** by **numeric order** on column **3**, with **header**, will return::
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216
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217 Fruit Color Price
5314e5d6f040 Imported from capsule None
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218 Apple Red 3.0
5314e5d6f040 Imported from capsule None
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219 Banana Yellow 4.1
5314e5d6f040 Imported from capsule None
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220 Melon Green 6.1
5314e5d6f040 Imported from capsule None
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221 Avocado Green 8.0
5314e5d6f040 Imported from capsule None
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222
5314e5d6f040 Imported from capsule None
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223
5314e5d6f040 Imported from capsule None
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224 -----
5314e5d6f040 Imported from capsule None
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225
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226 **Example - Natural vs. Alphabetical sorting**
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227
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228 Given the following list::
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229
5314e5d6f040 Imported from capsule None
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230 chr4
5314e5d6f040 Imported from capsule None
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231 chr13
5314e5d6f040 Imported from capsule None
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232 chr1
5314e5d6f040 Imported from capsule None
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233 chr10
5314e5d6f040 Imported from capsule None
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234 chr20
5314e5d6f040 Imported from capsule None
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235 chr2
5314e5d6f040 Imported from capsule None
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236
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237 **Alphabetical sort** would produce the following sorted list::
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238
5314e5d6f040 Imported from capsule None
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239 chr1
5314e5d6f040 Imported from capsule None
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240 chr10
5314e5d6f040 Imported from capsule None
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241 chr13
5314e5d6f040 Imported from capsule None
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242 chr2
5314e5d6f040 Imported from capsule None
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243 chr20
5314e5d6f040 Imported from capsule None
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244 chr4
5314e5d6f040 Imported from capsule None
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245
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246 **Natural Sort** would produce the following sorted list::
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247
5314e5d6f040 Imported from capsule None
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248 chr1
5314e5d6f040 Imported from capsule None
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249 chr2
5314e5d6f040 Imported from capsule None
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250 chr4
5314e5d6f040 Imported from capsule None
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251 chr10
5314e5d6f040 Imported from capsule None
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252 chr13
5314e5d6f040 Imported from capsule None
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253 chr20
5314e5d6f040 Imported from capsule None
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254
5314e5d6f040 Imported from capsule None
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255
5314e5d6f040 Imported from capsule None
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256 .. class:: infomark
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257
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258 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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259
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260 -----
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261
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262 **Example - Sorting based on parts of column values**
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263
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264 The above column of chromosomes, with their constant prefix, could have been sorted in natural order also with the **Fast numeric sort** and **considering its characters from** character 4 only.
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265
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266 In general, sorting based on just a range of characters in a column can be useful for sorting values with internal structure, in a single tool run.
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267
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268 Consider, for example, the following column of dates, which is unfortunately not ISO-8601 formatted::
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269
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270 10/24/2025
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271 09/18/1974
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272 12/16/1998
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273 03/04/2007
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274
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275 You could modify these values with other tools first, but you can achieve correct chronological sort order with a single run of the sort tool like this:
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276
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277 - Do a **Fast numeric sort** on the column **considering its characters from** character 7 (the start of the year).
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278 - Resolve ties (using another column selection section) with another **Fast numeric sort** on the same column **considering its characters from** character 1 **to and including** character 2 (the month representation).
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279 - Resolve remaining ties with a third **Fast numeric sort** on again the same column **considering its characters from** character 4 **to and including** character 5 (the day representation).
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280
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281 This will result in the ascending chronological order::
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282
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283 09/18/1974
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284 11/17/1998
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285 11/18/1998
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286 12/16/1998
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287 03/04/2007
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288 10/24/2025
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289
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290 Before relying on in-column character ranges, make extra sure that all values are formatted consistently (in the above example, that all dates use two digits for days and months and the same overall date format).
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291 ]]>
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292 </help>
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293 <expand macro="citations" />
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294 </tool>