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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="samtools_view_header" name="Samtools view header">
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3 <description>Show only the header of a BAM or SAM file using samtools.</description>
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4 <requirements>
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5 <requirement type="package" version="5.9">ncurses</requirement>
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6 <requirement type="package" version="0.1.19">samtools</requirement>
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7 </requirements>
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8 <command>
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9 samtools
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10 view
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11 -H
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12 #if $alignment.dataset.ext.lower() == "sam"
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13 -S
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14 #end if
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15 $alignment > $header 2> stderr.txt ;
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16
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17 cat stderr.txt
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18 </command>
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19
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20 <inputs>
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21 <param format="sam,bam" name="alignment" type="data" label="Alignment in BAM or SAM format" />
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22 </inputs>
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23
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24 <outputs>
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25 <data format="tabular" name="header" label="${tool.name} on ${alignment.name}" />
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26 </outputs>
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27
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28 <help>
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29 **samtools_view_header**
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30
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31 **Input formats**
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32
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33 * BAM
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34 * SAM
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35
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36 **Output format**
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37
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38 The SAM header as defined in the SAM specification. If the output is empty, there was no header in the alignment
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39
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40
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41 **Installation**
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42
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43 The installation is straight-forward and should go automatically using the Galaxy tool-shed installer.
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44
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45 **License**
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46
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47 * samtools: MIT License
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48
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49 **Contact**
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50
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51 The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
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52 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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53
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54 More tools by the Translational Research IT (TraIT) project can be found in the following repository:
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55 http://toolshed.dtls.nl/
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56 </help>
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57 </tool> |
