Mercurial > repos > bgruening > text_processing
annotate sort.xml @ 8:fa7f88da29d7 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
| author | bgruening |
|---|---|
| date | Tue, 30 Jun 2015 16:20:05 -0400 |
| parents | d64eace4f9f3 |
| children | c78b1767db2b |
| rev | line source |
|---|---|
| 4 | 1 <tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.0"> |
| 1 | 2 <description>data in ascending or descending order</description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"> | |
| 0 | 7 <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> |
| 4 | 8 </expand> |
| 9 <version_command>sort --version | head -n 1</version_command> | |
| 10 <command> | |
| 11 <![CDATA[ | |
| 12 ( | |
| 6 | 13 LC_ALL=C |
| 4 | 14 #if int($header) > 0: |
| 7 | 15 sed -u '${header}'q && |
| 4 | 16 #end if |
| 0 | 17 |
| 4 | 18 sort $unique $ignore_case --stable -t ' ' |
| 0 | 19 |
| 4 | 20 #for $key in $sortkeys: |
| 21 -k '${key.column}${key.order}${key.style},${key.column}' | |
| 22 #end for | |
| 0 | 23 |
| 4 | 24 ) < '${infile}' > '${outfile}' |
| 25 ]]> | |
| 0 | 26 </command> |
| 27 <inputs> | |
| 4 | 28 <param format="tabular" name="infile" type="data" label="Sort Query" /> |
| 29 <param name="header" type="integer" size="5" value="0" | |
| 30 label="Number of header lines" help="These will be ignored during sort."> | |
| 0 | 31 <validator type="in_range" message="Negative values are not allowed." min="0"/> |
| 32 </param> | |
| 33 | |
| 1 | 34 <repeat name="sortkeys" title="Column selections" min="1"> |
| 0 | 35 <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" /> |
| 36 <param name="order" type="select" display="radio" label="in"> | |
| 37 <option value="">Ascending order</option> | |
| 38 <option value="r">Descending order</option> | |
| 39 </param> | |
| 40 <param name="style" type="select" display="radio" label="Flavor"> | |
| 4 | 41 <option value="n">Fast numeric sort (-n)</option> |
| 42 <option value="g">General numeric sort ( scientific notation -g)</option> | |
| 43 <option value="V">Natural/Version sort (-V) </option> | |
| 0 | 44 <option value="">Alphabetical sort</option> |
| 45 <option value="h">Human-readable numbers (-h)</option> | |
| 4 | 46 <option value="R">Random order (-R)</option> |
| 0 | 47 </param> |
| 48 </repeat> | |
| 1 | 49 |
| 50 <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue="" | |
| 4 | 51 label="Output unique values" help="Print only unique values, based on sorted key columns. See help section for details. (--unique)" /> |
| 52 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" | |
| 53 label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters. (-i)" /> | |
| 0 | 54 </inputs> |
| 55 <outputs> | |
| 6 | 56 <data name="outfile" format_source="infile" metadata_source="infile"/> |
| 0 | 57 </outputs> |
| 1 | 58 <tests> |
| 59 <test> | |
| 6 | 60 <param name="infile" value="sort1.bed"/> |
| 4 | 61 <param name="header" value="3"/> |
| 62 <repeat name="sortkeys"> | |
| 63 <param name="column" value="1"/> | |
| 64 <param name="style" value=""/> | |
| 65 <param name="order" value=""/> | |
| 66 </repeat> | |
| 67 <repeat name="sortkeys"> | |
| 68 <param name="column" value="3"/> | |
| 69 <param name="style" value="n"/> | |
| 70 <param name="order" value="r"/> | |
| 71 </repeat> | |
| 72 <output name="outfile" file="sort_result1.bed"/> | |
| 1 | 73 </test> |
| 74 <test> | |
| 6 | 75 <param name="infile" value="sort1.bed"/> |
| 4 | 76 <param name="header" value="3"/> |
| 77 <repeat name="sortkeys"> | |
| 78 <param name="column" value="1"/> | |
| 79 <param name="style" value=""/> | |
|
8
fa7f88da29d7
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
bgruening
parents:
7
diff
changeset
|
80 <param name="order" value=""/> |
| 4 | 81 </repeat> |
| 82 <repeat name="sortkeys"> | |
| 83 <param name="column" value="3"/> | |
| 84 <param name="style" value="n"/> | |
| 85 <param name="order" value=""/> | |
| 86 </repeat> | |
| 87 <output name="outfile" file="sort_result2.bed"/> | |
| 1 | 88 </test> |
| 89 <test> | |
| 6 | 90 <param name="infile" value="sort2.bed"/> |
| 4 | 91 <repeat name="sortkeys"> |
| 92 <param name="column" value="5"/> | |
| 93 <param name="style" value="g"/> | |
| 94 <param name="order" value=""/> | |
| 95 </repeat> | |
| 96 <output name="outfile" file="sort_result3.bed"/> | |
| 1 | 97 </test> |
| 98 </tests> | |
| 0 | 99 <help> |
| 4 | 100 <![CDATA[ |
| 0 | 101 **What it does** |
| 102 | |
| 103 This tool sorts an input file. | |
| 104 | |
| 105 ----- | |
| 106 | |
| 107 **Sorting Styles** | |
| 108 | |
| 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). | |
| 110 * **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary. | |
| 111 * **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below. | |
| 112 * **Alphabetical sort**: Sort in strict alphabetical order. See example below. | |
| 113 * **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400) | |
| 114 * **Random order**: return lines in random order. | |
| 115 | |
| 116 ------ | |
| 117 | |
| 118 **Example - Header line** | |
| 119 | |
| 120 **Input file** (note first line is a header line, should not be sorted):: | |
| 121 | |
| 122 Fruit Color Price | |
| 123 Banana Yellow 4.1 | |
| 124 Avocado Green 8.0 | |
| 125 Apple Red 3.0 | |
| 126 Melon Green 6.1 | |
| 127 | |
| 128 **Sorting** by **numeric order** on column **3**, with **header**, will return:: | |
| 129 | |
| 130 Fruit Color Price | |
| 131 Apple Red 3.0 | |
| 132 Banana Yellow 4.1 | |
| 133 Melon Green 6.1 | |
| 134 Avocado Green 8.0 | |
| 135 | |
| 136 | |
| 137 ----- | |
| 138 | |
| 139 **Example - Natural vs. Alphabetical sorting** | |
| 140 | |
| 141 Given the following list:: | |
| 142 | |
| 143 chr4 | |
| 144 chr13 | |
| 145 chr1 | |
| 146 chr10 | |
| 147 chr20 | |
| 148 chr2 | |
| 149 | |
| 150 **Alphabetical sort** would produce the following sorted list:: | |
| 151 | |
| 152 chr1 | |
| 153 chr10 | |
| 154 chr13 | |
| 155 chr2 | |
| 156 chr20 | |
| 157 chr4 | |
| 158 | |
| 159 **Natural Sort** would produce the following sorted list:: | |
| 160 | |
| 161 chr1 | |
| 162 chr2 | |
| 163 chr4 | |
| 164 chr10 | |
| 165 chr13 | |
| 166 chr20 | |
| 167 | |
| 168 | |
| 169 .. class:: infomark | |
| 170 | |
| 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. | |
| 172 | |
| 4 | 173 @REFERENCES@ |
| 174 ]]> | |
| 0 | 175 </help> |
| 176 </tool> |