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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" version="0.1.19.a">
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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
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9 <version_command>samtools 2>&1 | grep -i "version:"</version_command>
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10
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11 <command>
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12 samtools
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13 view
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14 -H
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15 #if $alignment.dataset.ext.lower() == "sam"
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16 -S
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17 #end if
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18 $alignment > $header 2> stderr.txt ;
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19
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20 cat stderr.txt
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21 </command>
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22
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23 <inputs>
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24 <param format="sam,bam" name="alignment" type="data" label="Alignment in BAM or SAM format" />
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25 </inputs>
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26
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27 <outputs>
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28 <data format="tabular" name="header" label="${tool.name} on ${alignment.name}" />
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29 </outputs>
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30
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31 <help>
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32 **samtools_view_header**
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33
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34 **Input formats**
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35
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36 * BAM
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37 * SAM
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38
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39 **Output format**
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40
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41 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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42
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43
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44 **Installation**
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45
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46 The installation is straight-forward and should go automatically using the Galaxy tool-shed installer.
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47
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48 **License**
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49
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50 * samtools: MIT License
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51
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52 Contact
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53 -------
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54
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55 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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56 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
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57 Research IT (TraIT) project:
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58
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59 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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60
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61 More tools by the Translational Research IT (TraIT) project can be found
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62 in the following toolsheds:
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63
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64 http://toolshed.dtls.nl/
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65
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66 http://toolshed.g2.bx.psu.edu
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67
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68 http://testtoolshed.g2.bx.psu.edu/
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69 </help>
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70 </tool> |
