diff seqtk_mergepe.xml @ 0:e0a0fd938de4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_mergepe.xml	Thu Feb 05 11:52:40 2015 -0500
@@ -0,0 +1,93 @@
+<?xml version="1.0"?>
+<tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
+  <description>interleave two unpaired FASTA/Q files for a paired-end file</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[seqtk mergepe
+      $in_fq1
+      $in_fq2
+> $default]]></command>
+  <inputs>
+    <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
+    <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
+  </inputs>
+  <outputs>
+      <data format_source="in_fq1" hidden="false" name="default" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="in_fq1" value="paired_dat1.fq"/>
+      <param name="in_fq2" value="paired_dat2.fq"/>
+      <output name="default" file="paired_dat.fq" ftype="fastq"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+**What it does**
+
+Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
+
+::
+
+    # r1.fq
+    @test-6/1
+    AGCTTGACGC
+    +
+    ?.HCF@C>>F
+
+    # r2.fq
+    @test-6/2
+    TGCGAAGACC
+    +
+    >2?A?A@@7?
+
+will produce the following paired file:
+
+::
+
+    @test-6/1
+    AGCTTGACGC
+    +
+    ?.HCF@C>>F
+    @test-6/2
+    TGCGAAGACC
+    +
+    >2?A?A@@7?
+
+While this may not have been an illuminating example, it is important to note
+that this tool will properly interleave data. For example if you have the ids:
+
+::
+
+    @r-1/1
+    @r-2/1
+    @r-3/1
+    @r-4/1
+
+and
+
+::
+
+    @r-1/2
+    @r-2/2
+    @r-3/2
+    @r-4/2
+
+These will be interleaved as
+
+::
+
+    @r-1/1
+    @r-1/2
+    @r-2/1
+    @r-2/2
+    @r-3/1
+    @r-3/2
+    @r-4/1
+    @r-4/2
+
+@ATTRIBUTION@
+]]></help>
+</tool>