diff sort.xml @ 1:a4ad586d1403 draft

Uploaded
author bgruening
date Thu, 05 Sep 2013 11:42:27 -0400
parents ec66f9d90ef0
children 7068d1548234
line wrap: on
line diff
--- a/sort.xml	Thu Sep 05 04:58:21 2013 -0400
+++ b/sort.xml	Thu Sep 05 11:42:27 2013 -0400
@@ -1,4 +1,5 @@
 <tool id="unixtools_sort_header_tool" name="Sort" version="0.1.1">
+    <description>data in ascending or descending order</description>
     <requirements>
         <requirement type="package" version="8.21">gnu_coreutils</requirement>
         <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
@@ -25,16 +26,11 @@
 
     <inputs>
         <param format="txt" name="infile" type="data" label="Sort Query" />
-        <param name="header" type="integer" size="5" value="1" label="Number of header lines" help="These will be ignored during sort.">
+        <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>
 
-        <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." />
-
-        <repeat name="sortkeys" title="sort key">
+        <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>
@@ -49,12 +45,46 @@
                 <option value="R">Random order</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." />
+
     </inputs>
-    <tests>
-    </tests>
     <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"/>
+        </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"/>
+        </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"/>
+        </test>
+    </tests>
     <help>
 
 **What it does**