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annotate bam_stat.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 reads mapping statistics for a provided BAM or SAM file.
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4 </description>
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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5 <expand macro="bio_tools"/>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
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14 <version_command><![CDATA[bam_stat.py --version]]></version_command>
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16 <command><![CDATA[
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17 @BAM_SAM_INPUTS@
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18 bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}'
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19 ]]>
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20 </command>
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21
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22 <inputs>
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23 <expand macro="bam_sam_param" />
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24 <expand macro="mapq_param" />
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25 </inputs>
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26
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27 <outputs>
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28 <data format="txt" name="output" />
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29 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 <output name="output" file="output.bamstats.txt" />
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35 </test>
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36 </tests>
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38 <help><![CDATA[
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39 bam_stat.py
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40 +++++++++++
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41
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42 This program is used to calculate reads mapping statistics from provided BAM
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43 file. This script determines "uniquely mapped reads" from `mapping quality
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44 <http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
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45 which quality the probability that a read is misplaced (Do NOT confused with
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46 sequence quality, sequence quality measures the probability that a base-calling
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47 was wrong) .
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48
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49 Inputs
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50 ++++++++++++++
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51
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52 Input BAM/SAM file
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53 Alignment file in BAM/SAM format.
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55 Minimum mapping quality
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56 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
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57
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58 Output
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59 ++++++++++++++
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60
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61 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
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62 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
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63 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
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64 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
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65
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66 @ABOUT@
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67
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68 ]]>
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69 </help>
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71 <expand macro="citations" />
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72 </tool>