diff seqtk_hety.xml @ 15:16f2535c08bf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d

--- a/seqtk_hety.xml	Sat Oct 17 04:04:18 2015 -0400
+++ b/seqtk_hety.xml	Mon Jun 05 13:26:30 2017 -0400
@@ -1,33 +1,36 @@
 <?xml version="1.0"?>
 <tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0">
-  <description>regional heterozygosity</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk hety -w $w
+    <description>regional heterozygosity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk hety
+-w $w
 -t $t
 $m
-$in_file | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="window size" help="(-w)" name="w" type="integer" value="50000"/>
-    <param label="# start positions in a window" help="(-t)" name="t" type="integer" value="5"/>
-    <param checked="false" label="treat lowercases as masked" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Heterozygous regions in $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_hety.fa"/>
-      <param name="w" value="8"/>
-      <output name="default" file="seqtk_hety.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file' | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param argument="-w" type="integer" value="50000" label="Window size" />
+        <param argument="-t" type="integer" value="5" label="# start positions in a window" />
+        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Treat lowercases as masked" />
+    </inputs>
+    <outputs>
+        <data name="default" format="tabular" label="Heterozygous regions in $in_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_hety.fa"/>
+            <param name="w" value="8"/>
+            <output name="default" file="seqtk_hety.out" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Reports on heterozygosity over a region
@@ -69,6 +72,6 @@
 If you know what A and B are measures of, please `submit an issue <https://github.com/galaxyproject/tools-iuc/issues>`__ and it will be corrected
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>