Mercurial > repos > iuc > seqtk

diff seqtk_cutN.xml @ 15:16f2535c08bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:26:30 -0400
parents 55e75a28fde7
children 48a51c72f5e7
line wrap: on
line diff
--- a/seqtk_cutN.xml	Sat Oct 17 04:04:18 2015 -0400
+++ b/seqtk_cutN.xml	Mon Jun 05 13:26:30 2017 -0400
@@ -1,33 +1,36 @@
 <?xml version="1.0"?>
 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
-  <description>cut sequence at long N</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk cutN -n $n
+    <description>cut sequence at long N</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk cutN
+-n $n
 -p $p
 $g
-$in_file
-> $default]]></command>
-  <inputs>
-    <expand macro="in_faq"/>
-    <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
-    <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
-    <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
-  </inputs>
-  <outputs>
-    <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_cutn.fa"/>
-      <param name="n" value="1"/>
-      <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
+        <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
+        <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
+    </inputs>
+    <outputs>
+        <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_cutn.fa"/>
+            <param name="n" value="1"/>
+            <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Splits long sequences with runs of Ns
@@ -46,8 +49,7 @@
     >test:29-33
     ACATG
 
-
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>