diff seqtk_trimfq.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_trimfq.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@WRAPPER_VERSION@.0">
+  <description>trim FASTQ using the Phred algorithm</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk trimfq
+#if $mode.mode_select == "quality":
+-q $mode.q
+-l $mode.l
+#else:
+-b $mode.b
+-e $mode.e
+#end if
+$in_file
+> $default]]></command>
+  <inputs>
+    <expand macro="in_faq"/>
+    <conditional name="mode">
+        <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
+            <option value="quality">Quality</option>
+            <option value="position">Length/Position</option>
+        </param>
+        <when value="quality">
+            <param label="error rate threshold" help="(-q)" name="q" type="float" value="0.05"/>
+            <param label="maximally trim down to INT bp" help="(-l)" name="l" type="integer" value="30"/>
+        </when>
+        <when value="position">
+            <param label="trim INT bp from left" help="(-b)" name="b" type="integer" value="0"/>
+            <param label="trim INT bp from right" help="(-e)" name="e" type="integer" value="0"/>
+        </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format_source="in_file" hidden="false" name="default" label="$in_file.name trimmed"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_file" value="seqtk_trimfq.fq"/>
+      <param name="mode_select" value="quality"/>
+      <param name="q" value="0.05"/>
+      <param name="l" value="30"/>
+      <output name="default" file="seqtk_trimfq_default.fq" ftype="fastq"/>
+    </test>
+    <test>
+      <param name="in_file" value="seqtk_trimfq.fq"/>
+      <param name="mode_select" value="position"/>
+      <param name="b" value="5"/>
+      <param name="e" value="5"/>
+      <output name="default" file="seqtk_trimfq_be.fq" ftype="fastq"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Trim a fastq file based on Phred scores, or by length
+
+@ATTRIBUTION@
+]]></help>
+</tool>