Mercurial > repos > tiagoantao > barcode_stacks

annotate barcode_sort.xml @ 9:1bce4c0c9369 draft

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author tiagoantao
date Thu, 31 Mar 2016 10:34:04 -0400
parents 8b0f010d356c
children f153f82e6d3a
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1 <tool id="barcode_sort_stacks" name="Barcode sorting for Stacks" version="2.0.0" force_history_refresh="True">
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2 <description>Barcode Sorting with Paired-End reads for Stacks</description>
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4 <stdio>
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5 <exit_code range="1" level="fatal" description="Error in script execution" />
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6 </stdio>
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8 <command interpreter="perl">
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10 barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded $barcode_length $cut_site
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12 </command>
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14 <inputs>
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15 <param name="barcode" format="text" type="data" label="Barcode file" />
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16 <param name="barcode_length" type="integer" value="6" label="Barcode length" />
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17 <param name="f1" type="data" format="fastq" label="First read FASTQ" />
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18 <param name="f2" type="data" format="fastq" label="Second read FASTQ" />
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19 <param name="cut_site" type="text" value="TGCA" label="Cut site" />
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20 </inputs>
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21 <outputs>
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22 <data format="fastq" name="barcoded" label="Barcoded sequences"/>
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23 <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
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24 </outputs>
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25
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26 <help>
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27
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28 .. class:: infomark
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29
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30 **What it does**
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31
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32 This program takes 2 input sequence files where the barcode can be on either
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33 the 1st or 2nd read (but not both) and sorts all barcoded reads into a single
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34 file and all non-barcoded files into a second file. This separation is needed
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35 for the STACKs program as it does not handle sequences where the barcode is
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36 arbitrarily on the 1st or 2nd read.
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38 --------
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39
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40 **Created by:**
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41
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42 Paul Hohenlohe with changes from Brian Hand.
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43
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44 **Integrated by:**
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46 Tiago Antao
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48
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49 </help>
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50
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51 </tool>