Mercurial > repos > tiagoantao > barcode_stacks

annotate barcode_sort.xml @ 0:d838c6a2ec0f draft

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author tiagoantao
date Mon, 28 Mar 2016 18:46:00 -0400
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1 <tool id="barcode_sort_stacks" name="Barcode sorting for Stacks" version="1.0.0" force_history_refresh="True">
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2 <description>Run the STACKS populations program</description>
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5 <requirements>
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6 <requirement type="package" version="5.18">perl</requirement>
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7 </requirements>
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11 <stdio>
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12 <exit_code range="1" level="fatal" description="Error in script execution" />
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13 </stdio>
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15 <command interpreter="perl">
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17 barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded
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19 </command>
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21 <inputs>
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22 <param name="barcode" format="txt" type="data" label="Barcode file 1" />
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23 <param name="f1" format="fastq" label="First reads" />
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24 <param name="f2" format="fastq" label="Second reads" />
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25 </inputs>
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26 <outputs>
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27 <data format="fastq" name="barcoded" label="Barcoded sequences"/>
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28 <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
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29 </outputs>
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30
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31 <help>
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32
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33 .. class:: infomark
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34
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35 **What it does**
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37 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.
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38
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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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46
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47 Tiago Antao
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49
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50 </help>
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51
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52 <citations>
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53 </citations>
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54 </tool>
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