diff seqtk_dropse.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_dropse.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,76 @@
+<?xml version="1.0"?>
+<tool id="seqtk_dropse" name="seqtk_dropse" version="@WRAPPER_VERSION@.0">
+  <description>drop unpaired from interleaved Paired End FASTA/Q</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk dropse
+      $in_file
+> $default]]></command>
+  <inputs>
+    <expand macro="in_faq"/>
+  </inputs>
+  <outputs>
+    <data format_source="in_file" hidden="false" name="default" label="Only paired-end reads from $in_file.name"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_file" value="seqtk_dropse.fq"/>
+      <output name="default" file="seqtk_dropse.out" ftype="fastq"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Remove unpaired reads in an interleaved paired-end FASTA/Q file. Given a fastq file with unpaired reads:
+
+::
+
+    @test-6/1
+    AGCTTGACGC
+    +
+    ?.HCF@C>>F
+    @test-6/2
+    TGCGAAGACC
+    +
+    >2?A?A@@7?
+    @test-4/1
+    CTTGACGCTG
+    +
+    I@>3EFCG@C
+    @test-2/1
+    AGACCAAAAT
+    +
+    ??><6E?IFC
+    @test-2/2
+    CTGGCGAATT
+    +
+    ?=?*?A?<?@
+
+This tool will remove the offending reads (test-4/1), leaving just the paired data.
+
+::
+
+    @test-6/1
+    AGCTTGACGC
+    +
+    ?.HCF@C>>F
+    @test-6/2
+    TGCGAAGACC
+    +
+    >2?A?A@@7?
+    @test-2/1
+    AGACCAAAAT
+    +
+    ??><6E?IFC
+    @test-2/2
+    CTGGCGAATT
+    +
+    ?=?*?A?<?@
+
+
+@ATTRIBUTION@
+      ]]></help>
+</tool>