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1 <tool id="bamsort" name="Sort BAM file">
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2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
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2
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3 <macros>
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4 <import>toolshed_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>mimodd version -q</version_command>
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8 <command>
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9 mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name
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10 </command>
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11
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12 <inputs>
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13 <param name="inputfile" type="data" format="bam" label="Input file to sort" />
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14 <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
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15 <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
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16 </inputs>
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17
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18 <outputs>
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19 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
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20 <change_format>
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21 <when input="oformat" value="sam" format="sam" />
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22 </change_format>
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23 </data>
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24 </outputs>
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25
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26 <help>
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27 .. class:: infomark
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28
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29 **What it does**
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30
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31 The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
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32
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33 Coordinate-sorted input files are expected by most downstream MiModD tools, but note that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order.
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34
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35 The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
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36
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37 </help>
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38 </tool>
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39
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