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annotate samtools_flagstat.xml @ 9:5fbe9dcaef98 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
author iuc
date Fri, 06 Sep 2019 11:21:12 -0400
parents 5fd05c7b42f8
children 9b44224f5a76
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5fbe9dcaef98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
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1 <tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.3">
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2 <description>tabulate descriptive stats for BAM datset</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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11 <command><![CDATA[
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12 @ADDTHREADS@
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13 samtools flagstat -@ \$addthreads '$input1' > '$output1'
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14 ]]></command>
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16 <inputs>
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17 <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" />
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18 </inputs>
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20 <outputs>
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21 <data name="output1" format="txt" />
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22 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
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27 <output name="output1" file="samtools_flagstat_out1.txt" />
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
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34
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35 200 + 0 in total (QC-passed reads + QC-failed reads)
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36 0 + 0 secondary
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37 0 + 0 supplementary
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38 0 + 0 duplicates
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39 25 + 0 mapped (12.50%:nan%)
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40 200 + 0 paired in sequencing
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41 100 + 0 read1
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42 100 + 0 read2
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43 0 + 0 properly paired (0.00%:nan%)
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44 0 + 0 with itself and mate mapped
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45 25 + 0 singletons (12.50%:nan%)
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46 0 + 0 with mate mapped to a different chr
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47 0 + 0 with mate mapped to a different chr (mapQ>=5)
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5fbe9dcaef98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
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49 The results of samtools flagstat can be visualized with MultiQC.
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50 ]]></help>
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51 <expand macro="citations"/>
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52 </tool>