diff sort.xml @ 0:5314e5d6f040 draft

Imported from capsule None

--- /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>