Mercurial > repos > bgruening > text_processing
diff sort.xml @ 0:5314e5d6f040 draft
Imported from capsule None
author | bgruening |
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date | Thu, 29 Jan 2015 07:53:17 -0500 |
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children | 43b1f073b693 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sort.xml Thu Jan 29 07:53:17 2015 -0500 @@ -0,0 +1,176 @@ +<tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.0"> + <description>data in ascending or descending order</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> + </expand> + <version_command>sort --version | head -n 1</version_command> + <command> +<![CDATA[ + ( + LC_ALL=C + #if int($header) > 0: + sed -u '${header}'q && + #end if + + sort $unique $ignore_case --stable -t ' ' + + #for $key in $sortkeys: + -k '${key.column}${key.order}${key.style},${key.column}' + #end for + + ) < '${infile}' > '${outfile}' +]]> + </command> + <inputs> + <param format="tabular" name="infile" type="data" label="Sort Query" /> + <param name="header" type="integer" size="5" value="0" + label="Number of header lines" help="These will be ignored during sort."> + <validator type="in_range" message="Negative values are not allowed." min="0"/> + </param> + + <repeat name="sortkeys" title="Column selections" min="1"> + <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" /> + <param name="order" type="select" display="radio" label="in"> + <option value="">Ascending order</option> + <option value="r">Descending order</option> + </param> + <param name="style" type="select" display="radio" label="Flavor"> + <option value="n">Fast numeric sort (-n)</option> + <option value="g">General numeric sort ( scientific notation -g)</option> + <option value="V">Natural/Version sort (-V) </option> + <option value="">Alphabetical sort</option> + <option value="h">Human-readable numbers (-h)</option> + <option value="R">Random order (-R)</option> + </param> + </repeat> + + <param name="unique" type="boolean" checked="false" truevalue="--unique" falsevalue="" + label="Output unique values" help="Print only unique values, based on sorted key columns. See help section for details. (--unique)" /> + <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" + label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters. (-i)" /> + </inputs> + <outputs> + <data name="outfile" format_source="infile" metadata_source="infile"/> + </outputs> + <tests> + <test> + <param name="infile" value="sort1.bed"/> + <param name="header" value="3"/> + <repeat name="sortkeys"> + <param name="column" value="1"/> + <param name="style" value=""/> + <param name="order" value=""/> + </repeat> + <repeat name="sortkeys"> + <param name="column" value="3"/> + <param name="style" value="n"/> + <param name="order" value="r"/> + </repeat> + <output name="outfile" file="sort_result1.bed"/> + </test> + <test> + <param name="infile" value="sort1.bed"/> + <param name="header" value="3"/> + <repeat name="sortkeys"> + <param name="column" value="1"/> + <param name="style" value=""/> + <param name="order" value=""/> + </repeat> + <repeat name="sortkeys"> + <param name="column" value="3"/> + <param name="style" value="n"/> + <param name="order" value=""/> + </repeat> + <output name="outfile" file="sort_result2.bed"/> + </test> + <test> + <param name="infile" value="sort2.bed"/> + <repeat name="sortkeys"> + <param name="column" value="5"/> + <param name="style" value="g"/> + <param name="order" value=""/> + </repeat> + <output name="outfile" file="sort_result3.bed"/> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +This tool sorts an input file. + +----- + +**Sorting Styles** + +* **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). +* **General Numeric**: sort by numeric values. Handles all numeric notations (including scientific notation). Slower than *fast numeric*, so use only when necessary. +* **Natural Sort**: Sort in 'natural' order (natural to humans, not to computers). See example below. +* **Alphabetical sort**: Sort in strict alphabetical order. See example below. +* **Human-readable numbers**: Sort human readble numbers (e.g. 1G > 2M > 3K > 400) +* **Random order**: return lines in random order. + +------ + +**Example - Header line** + +**Input file** (note first line is a header line, should not be sorted):: + + Fruit Color Price + Banana Yellow 4.1 + Avocado Green 8.0 + Apple Red 3.0 + Melon Green 6.1 + +**Sorting** by **numeric order** on column **3**, with **header**, will return:: + + Fruit Color Price + Apple Red 3.0 + Banana Yellow 4.1 + Melon Green 6.1 + Avocado Green 8.0 + + +----- + +**Example - Natural vs. Alphabetical sorting** + +Given the following list:: + + chr4 + chr13 + chr1 + chr10 + chr20 + chr2 + +**Alphabetical sort** would produce the following sorted list:: + + chr1 + chr10 + chr13 + chr2 + chr20 + chr4 + +**Natural Sort** would produce the following sorted list:: + + chr1 + chr2 + chr4 + chr10 + chr13 + chr20 + + +.. class:: infomark + +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. + +@REFERENCES@ +]]> + </help> +</tool>