Mercurial > repos > iuc > seqtk

diff seqtk_fqchk.xml @ 3:bc7d99f46a5d 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 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
line wrap: on
line diff
--- a/seqtk_fqchk.xml	Fri Jan 01 14:49:42 2016 -0500
+++ b/seqtk_fqchk.xml	Mon Jun 05 13:27:11 2017 -0400
@@ -1,29 +1,31 @@
 <?xml version="1.0"?>
 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
-  <description>fastq QC (base/quality summary)</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <expand macro="stdio"/>
-  <command><![CDATA[seqtk fqchk
+    <description>fastq QC (base/quality summary)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk fqchk
 -q $q
-$in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
-> $default]]></command>
-  <inputs>
-    <expand macro="in_fq"/>
-    <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="in_file" value="seqtk_fqchk.fq"/>
-      <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
-    </test>
-  </tests>
-  <help><![CDATA[
+'$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_fq"/>
+        <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
+    </inputs>
+    <outputs>
+        <data name="default" format="tabular" label="Quality information for $in_file.name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_fqchk.fq"/>
+            <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Returns quality score information base-by-base.
@@ -54,6 +56,6 @@
     10    1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0
 
 @ATTRIBUTION@
-]]></help>
-  <expand macro="citation" />
+    ]]></help>
+    <expand macro="citation" />
 </tool>