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15
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1 <tool id="extract_aln_ends.py" name="Extract alignment ends." version="0.2.0">
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2 <description>from SAM or BAM.</description>
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56
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3 <requirements>
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58
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4 <requirement type="package" version="2.24">bedtools</requirement>
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5 <requirement type="package" version="0.7.4">pybedtools</requirement>
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56
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6 <requirement type="package" version="0.8.3">pysam</requirement>
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7 </requirements>
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0
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8 <macros>
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9 <import>macros.xml</import>
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10 </macros>
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11 <expand macro="stdio" />
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50
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12 <version_command>python $__tool_directory__/extract_aln_ends.py --version</version_command>
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0
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13 <command interpreter="python"><![CDATA[
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14 extract_aln_ends.py
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15 #if $positional_1 and $positional_1 is not None:
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16 $positional_1
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17 #end if
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18
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19 > $default]]></command>
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20 <inputs>
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14
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21 <param area="false" label="Alignments in SAM or BAM format." name="positional_1" type="data" format="sam,bam"/>
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0
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22 </inputs>
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23 <outputs>
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24 <data format="bed" hidden="false" name="default"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="positional_1" value="twomates.sam"/>
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29 <output name="default" file="tworeads_aln_ends.bed"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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14
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33 Extract alignment ends from bam file.
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0
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34
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35 The resulting bed file contains the outer coordinates of the alignments. The
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36 bed name field is set to the read id and the score field is set to the edit
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37 distance of the alignment. The crosslinked nucleotide is one nt upstream of the
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38 5'-end of the bed entries.
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39
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40 This tool only reports results for alignments that are properly aligned in FR
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41 ("forward-reverse") direction.
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42
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43 Input:
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6
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44
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45 * bam file containing alignments (paired-end sequencing)
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0
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46
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47 Output:
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6
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48
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0
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49 * bed6 file containing outer coordinates (sorted by read id)
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50
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51 Author: Daniel Maticzka
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52 Copyright: 2015
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53 License: Apache
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54 Email: maticzkd@informatik.uni-freiburg.de
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55 Status: Development
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56 ]]></help>
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57 <expand macro="citations" />
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58 </tool>
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