Mercurial > repos > bgruening > text_processing
diff sort.xml @ 4:56e80527c482 draft
Uploaded
| author | bgruening |
|---|---|
| date | Wed, 07 Jan 2015 11:10:52 -0500 |
| parents | 7068d1548234 |
| children | 8928e6d1e7ba |
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--- a/sort.xml Sun Oct 06 08:22:36 2013 -0400 +++ b/sort.xml Wed Jan 07 11:10:52 2015 -0500 @@ -1,32 +1,32 @@ -<tool id="tp_sort_header_tool" name="Sort" version="0.1.1"> +<tool id="tp_sort_header_tool" name="Sort" version="@BASE_VERSION@.0"> <description>data in ascending or descending order</description> - <requirements> - <requirement type="package" version="8.21">gnu_coreutils</requirement> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement> - </requirements> - <command interpreter="sh"> - #if int($header) > 0: - (sed -u '${header}'q && sort $unique $ignore_case --stable -t ' ' - - #for $key in $sortkeys - '-k ${key.column}${key.order}${key.style},${key.column}' - #end for + </expand> + <version_command>sort --version | head -n 1</version_command> + <command> +<![CDATA[ + ( + #if int($header) > 0: + sed -u '${header}'q && + #end if - ) < '${infile}' > '${outfile}' - #else: - (sort $unique $ignore_case --stable -t ' ' + sort $unique $ignore_case --stable -t ' ' - #for $key in $sortkeys - '-k ${key.column}${key.order}${key.style},${key.column}' - #end for + #for $key in $sortkeys: + -k '${key.column}${key.order}${key.style},${key.column}' + #end for - ) < '${infile}' > '${outfile}' - #end if + ) < '${infile}' > '${outfile}' +]]> </command> - <inputs> - <param format="txt" 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."> + <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> @@ -37,56 +37,67 @@ <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="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</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." /> - - <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." /> + 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 format="input" name="outfile" metadata_source="infile"/> </outputs> <tests> - <!-- anyone knows how to write tests with repeat tags --> <test> <param name="infile" value="sort_in1.bed"/> - <param name="column" value="1"/> - <param name="style" value=""/> - <param name="order" value="ASC"/> - <param name="other_column" value="3"/> - <param name="other_style" value="n"/> - <param name="other_order" value="r"/> - <output name="out_file1" file="sort_out1.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="sort_in1.bed"/> - <param name="column" value="1"/> - <param name="style" value=""/> - <param name="order" value="ASC"/> - <param name="other_column" value="3"/> - <param name="other_style" value="n"/> - <param name="other_order" value=""/> - <output name="out_file1" file="sort_out2.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="sort_in2.bed"/> - <param name="column" value="5"/> - <param name="style" value="g"/> - <param name="order" value=""/> - <output name="out_file1" file="sort_out3.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. @@ -159,9 +170,7 @@ 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. ------ - -*sort-header* is was written by A. Gordon ( gordon at cshl dot edu ) - +@REFERENCES@ +]]> </help> </tool>