comparison barcode_sort.xml @ 7:2c843c8df821 draft

planemo upload commit 1af8d398aa035883718d02bb1b9051edb5d10c48

6:5cd3cc89bf59

   <exit_code range="1" level="fatal" description="Error in script execution" />
</stdio>

<command interpreter="perl">

barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded

</command>

<inputs>
  <param name="barcode" format="txt" type="data" label="Barcode file 1" />
  <param name="f1" type="data" format="fastq" label="First reads" />
  <param name="f2" type="data" format="fastq" label="Second reads" />
</inputs>
<outputs>
  <data format="fastq" name="barcoded" label="Barcoded sequences"/>
  <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
</outputs>

.. class:: infomark

**What it does**

This program takes 2 input sequence files where the barcode can be on either the 1st or 2nd read (but not both) and sorts all barcoded reads into a single file and all non-barcoded files into a second file. This separation is needed for the STACKs program as it does not handle sequences where the barcode is arbitrarily on the 1st or 2nd read.

--------

**Created by:**

</help>

</tool>

7:2c843c8df821

   <exit_code range="1" level="fatal" description="Error in script execution" />
</stdio>

<command interpreter="perl">

barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded $barcode_length $cut_site

</command>

<inputs>
  <param name="barcode" format="txt" type="data" label="Barcode file" />
  <param name="barcode_length" type="integer" value="6" label="Barcode length" />
  <param name="f1" type="data" format="fastq" label="First read FASTQ" />
  <param name="f2" type="data" format="fastq" label="Second read FASTQ" />
  <param name="cut_site" type="txt" value="TGCA" label="Cut site" />
</inputs>
<outputs>
  <data format="fastq" name="barcoded" label="Barcoded sequences"/>
  <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
</outputs>

.. class:: infomark

**What it does**

This program takes 2 input sequence files where the barcode can be on either
the 1st or 2nd read (but not both) and sorts all barcoded reads into a single
file and all non-barcoded files into a second file. This separation is needed
for the STACKs program as it does not handle sequences where the barcode is
arbitrarily on the 1st or 2nd read.

--------

**Created by:**

</help>

</tool>