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1 <tool id="samtools_flagstat" name="Flagstat" version="2.0">
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2 <description>tabulate descriptive stats for BAM datset</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"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command>samtools flagstat "$input1" > "$output1"
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10 </command>
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11 <inputs>
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12 <param name="input1" type="data" format="bam" label="BAM File to Convert" />
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13 </inputs>
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14 <outputs>
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15 <data name="output1" format="txt" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
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20 <output name="output1" file="samtools_flagstat_out1.txt" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25 **What it does**
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26
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27 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
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28
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29 200 + 0 in total (QC-passed reads + QC-failed reads)
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30 0 + 0 secondary
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31 0 + 0 supplementary
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32 0 + 0 duplicates
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33 25 + 0 mapped (12.50%:nan%)
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34 200 + 0 paired in sequencing
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35 100 + 0 read1
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36 100 + 0 read2
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37 0 + 0 properly paired (0.00%:nan%)
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38 0 + 0 with itself and mate mapped
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39 25 + 0 singletons (12.50%:nan%)
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40 0 + 0 with mate mapped to a different chr
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41 0 + 0 with mate mapped to a different chr (mapQ>=5)
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42
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43 </help>
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44 <expand macro="citations"></expand>
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45 </tool>
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