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annotate bamtools_split_paired.xml @ 1:9dbf707bebb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
author iuc
date Wed, 11 Jan 2023 12:03:53 +0000
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9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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1 <tool id="bamtools_split_paired" name="Split BAM by Paired/Single End" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description></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>
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8 <![CDATA[
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9 ln -s '${input_bam}' 'localbam.bam' &&
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10 ln -s '${input_bam.metadata.bam_index}' 'localbam.bam.bai' &&
9dbf707bebb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split_ref commit a14db40361bcb2ee608bccd9222e1654aaea3324-dirty
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11 bamtools split -paired
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12 -in localbam.bam
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13 -stub split_bam
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="input_bam" type="data" format="bam" label="BAM dataset to split by single_end/paired_end"/>
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18 </inputs>
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19 <outputs>
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20 <data format="bam" name="single" label="${input_bam.name} mapped" from_work_dir="split_bam.SINGLE_END.bam" />
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21 <data format="bam" name="paired" label="${input_bam.name} unmapped" from_work_dir="split_bam.PAIRED_END.bam" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_bam" ftype="bam" value="bamtools-input-paired.bam"/>
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26 <output name="single" file="split_bam.SINGLE_END.bam" compare="sim_size" delta="200" />
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27 <output name="paired" file="split_bam.PAIRED_END.bam" compare="sim_size" delta="200" />
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28 </test>
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29 </tests>
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30 <help>
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31 **What is does**
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33 BAMTools split is a utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
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35 -----
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37 .. class:: warningmark
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40 **How it works**
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43 Splits the input BAM file into 2 output files named (SINGLE_END) and (PAIRED_END) containing single_end and paired_end reads, respectively.
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45 -----
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47 .. class:: infomark
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49 **More information**
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51 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki
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53 </help>
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54 <citations>
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55 <citation type="doi">10.1093/bioinformatics/btr174</citation>
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56 </citations>
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57 </tool>