Mercurial > repos > devteam > samtools_flagstat

annotate samtools_flagstat.xml @ 7:fe34990e5ce7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:13:41 +0000
parents 22970df7a40e
children fefd89ab563c
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fe34990e5ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1 <tool id="samtools_flagstat" name="Samtools flagstat" version="2.0.4" profile="@PROFILE@">
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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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fe34990e5ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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13 samtools flagstat -@ \$addthreads
fe34990e5ce7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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14 #if $output_fmt != 'txt'
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15 --output-fmt $output_fmt
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16 #end if
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17 '$input1'
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18 > '$output1'
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19 ]]></command>
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20
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21 <inputs>
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22 <param name="input1" type="data" format="sam,bam,cram" label="BAM File to report statistics of" />
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23 <param argument="--output-fmt" type="select" label="Output format">
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24 <option value="txt">txt</option>
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25 <option value="tsv">tsv</option>
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26 <option value="json">json</option>
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27 </param>
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28 </inputs>
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30 <outputs>
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31 <data name="output1" format="txt">
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32 <change_format>
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33 <when input="output_fmt" value="tsv" format="tabular" />
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34 <when input="output_fmt" value="json" format="json" />
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35 </change_format>
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36 </data>
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37 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
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42 <output name="output1" file="samtools_flagstat_out1.txt" ftype="txt"/>
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43 </test>
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44 <test>
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45 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
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46 <param name="output_fmt" value="tsv"/>
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47 <output name="output1" file="samtools_flagstat_out1.tsv" ftype="tabular" />
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48 </test>
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49 <test>
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50 <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
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51 <param name="output_fmt" value="json"/>
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52 <output name="output1" file="samtools_flagstat_out1.json" ftype="json" />
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 **What it does**
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57
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58 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
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59
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60 200 + 0 in total (QC-passed reads + QC-failed reads)
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61 0 + 0 secondary
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62 0 + 0 supplementary
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63 0 + 0 duplicates
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64 25 + 0 mapped (12.50%:nan%)
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65 200 + 0 paired in sequencing
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66 100 + 0 read1
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67 100 + 0 read2
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68 0 + 0 properly paired (0.00%:nan%)
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69 0 + 0 with itself and mate mapped
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70 25 + 0 singletons (12.50%:nan%)
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71 0 + 0 with mate mapped to a different chr
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72 0 + 0 with mate mapped to a different chr (mapQ>=5)
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74 The results of samtools flagstat can be visualized with MultiQC.
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75 ]]></help>
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76 <expand macro="citations"/>
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77 </tool>