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1 <tool id="bamsort" name="Sort BAM file" version="0.1.7.3">
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2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
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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 "$input.ifile" -o "$output" --iformat $input.iformat --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 <conditional name="input">
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14 <param label="Input data format" name="iformat" type="select">
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15 <option value="bam">bam</option>
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16 <option value="sam">sam</option>
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17 </param>
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18 <when value="bam">
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19 <param format="bam" label="BAM input file to sort" name="ifile" type="data" />
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20 </when>
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21 <when value="sam">
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22 <param format="sam" label="SAM input file to sort" name="ifile" type="data" />
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23 </when>
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24 </conditional>
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25 <param label="Output format for the sorted data" name="oformat" type="select">
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26 <option value="bam">bam</option>
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27 <option value="sam">sam</option>
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28 </param>
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29 <param checked="false" falsevalue="" 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." label="Sort by read names instead of coordinates" name="by_name" truevalue="-n" type="boolean" />
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30 </inputs>
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31
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32 <outputs>
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33 <data format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}" name="output">
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34 <change_format>
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35 <when format="sam" input="oformat" value="sam" />
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36 </change_format>
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37 </data>
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38 </outputs>
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39
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40 <help>
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41 .. class:: infomark
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42
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43 **What it does**
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44
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45 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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46
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47 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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48
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49 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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50
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51 </help>
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52 </tool>
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