Mercurial > repos > iuc > bctools_extract_alignment_ends

annotate extract_aln_ends.xml @ 3:cb9827c97502 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
author iuc
date Fri, 04 Oct 2024 08:55:45 +0000
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cb9827c97502 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a6a6774ae353f915a5ca34af8f281edd91e5c665
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1 <tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from SAM or BAM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 extract_aln_ends.py
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9 '$alignments'
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10 > '$alignment_ends'
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11 ]]></command>
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12 <inputs>
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13 <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/>
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14 </inputs>
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15 <outputs>
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16 <data name="alignment_ends" format="bed"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="alignments" value="twomates.sam"/>
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21 <output name="alignment_ends" file="tworeads_aln_ends.bed"/>
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22 </test>
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23 </tests>
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24 <help><![CDATA[
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26 bctools - Extract alignment ends from from SAM or BAM alignments
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27 ================================================================
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29 The resulting BED file contains the outer coordinates of the alignments. The BED
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30 name field is set to the read id and the score field is set to the edit distance
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31 of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of
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32 the BED entries.
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34 This tool only reports results for alignments that are properly aligned in FR
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35 ("forward-reverse") direction.
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37 Input:
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38 ------
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40 * BAM file containing alignments (paired-end sequencing)
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41
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42 Output:
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43 -------
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44
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45 * BED file containing outer coordinates (sorted by read id)
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46
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47 ]]></help>
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48 <expand macro="citations"/>
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49 </tool>