diff unsorted_uniq.xml @ 0:ec66f9d90ef0 draft

initial uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unsorted_uniq.xml	Thu Sep 05 04:58:21 2013 -0400
@@ -0,0 +1,79 @@
+<tool id="unixtools_sorted_uniq" name="Unique" version="0.3">
+  <description>occurrences of each record</description>
+    <requirements>
+        <requirement type="package" version="8.21">gnu_coreutils</requirement>
+    </requirements>
+    <command interpreter='python'>
+        unique_lines.py 
+            $ignore_case 
+            $is_numeric
+            #if $adv_opts.adv_opts_selector=="advanced":
+                $adv_opts.column_start
+                $adv_opts.column_end
+            #end if
+            $outfile
+            $infile
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="tabular,text" label="from query" /> 
+        <param name="ignore_case" type="boolean" label="ignore differences in case when comparing (-f)" truevalue="-f" falsevalue="false" checked="false" help="ignore differences in case when comparing"/>
+        <param name="is_numeric" type="boolean" label="column only contains numeric values (-n)" truevalue="-n" falsevalue="false" checked="false" help="did the calumn have numeric values"/>
+        <conditional name="adv_opts">
+            <param name="adv_opts_selector" type="select" label="Advanced Options">
+              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="advanced">Show Advanced Options</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
+                <param name="column_start" label="Column start" type="data_column" data_ref="infile" help="Unique on specific column range"/>
+                <param name="column_end" label="Column end" type="data_column" data_ref="infile" help="Unique on specific column range"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="infile" name="outfile" metadata_source="infile"/>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+ .. class:: infomark
+
+**Syntax**
+
+This tool returns all unique lines using the 'sort -u' command. It can be used with unsorted files. 
+If you need additional options, like grouping or counting your unique results, please use the 'Unique lines from sorted file' tool.
+
+-----
+
+.. class:: infomark
+
+The input file needs to be tab separated. Please convert your file if necessary.
+
+-----
+
+**Example**
+
+- Input file::
+     
+       chr1   10  100  gene1
+       chr1  105  200  gene2
+       chr1   10  100  gene1
+       chr2   10  100  gene4
+       chr2 1000 1900  gene5
+       chr3   15 1656  gene6
+       chr2   10  100  gene4
+
+- Unique lines will result in::
+
+       chr1   10  100  gene1
+       chr1  105  200  gene2
+       chr2   10  100  gene4
+       chr2 1000 1900  gene5
+       chr3   15 1656  gene6
+
+
+</help>
+</tool>