Mercurial > repos > tiagoantao > barcode_stacks

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author tiagoantao
date Sun, 03 Apr 2016 09:56:55 -0400
parents f153f82e6d3a
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1 <tool id="barcode_sort_stacks" name="Barcode sorting for Stacks" version="2.0.2" 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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7
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8 <command interpreter="perl">
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10 barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded true $barcode_length $cut_site $max_errors
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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 <param name="max_errors" type="integer" value="2" label="Maximum number of errors" />
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21 </inputs>
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22 <outputs>
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23 <data format="fastq" name="barcoded" label="Barcoded sequences"/>
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24 <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
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25 </outputs>
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26
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27 <help>
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28
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29 .. class:: infomark
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30
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31 **What it does**
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32
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33 This program takes 2 input sequence files where the barcode can be on either
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34 the 1st or 2nd read (but not both) and sorts all barcoded reads into a single
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35 file and all non-barcoded files into a second file. This separation is needed
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36 for the STACKs program as it does not handle sequences where the barcode is
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37 arbitrarily on the 1st or 2nd read.
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39 --------
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40
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41 **Created by:**
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42
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43 Paul Hohenlohe with changes from Brian Hand.
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44
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45 **Integrated by:**
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47 Tiago Antao
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50 </help>
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51
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52 </tool>