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1 <tool id="samtools_0_1_18_flagstat" name="flagstat" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="0.1.18">samtools</requirement>
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4 </requirements>
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5 <description>provides simple stats on BAM files</description>
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6 <command>samtools flagstat "$input1" > "$output1"
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7 </command>
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8 <inputs>
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9 <param name="input1" type="data" format="bam" label="BAM File" />
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10 </inputs>
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11 <outputs>
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12 <data name="output1" format="txt" />
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13 </outputs>
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14 <!--
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15 <tests>
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16 <test>
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17 <param name="input1" value="unsorted.bam" ftype="bam" />
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18 <output name="output1" file="samtools_flagstat_out1.txt" />
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19 </test>
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20 </tests>
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21 -->
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22 <help>
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23
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24 This tool runs the flagstat command of samtools 0.1.18 to produce simple stats on a BAM file.
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25
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26 </help>
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27 </tool>
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