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annotate bam_stat.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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a7f9084572fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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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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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="bio_tools"/>
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11 <expand macro="requirements" />
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13 <expand macro="stdio" />
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15 <version_command><![CDATA[bam_stat.py --version]]></version_command>
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17 <command><![CDATA[
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18 @BAM_SAM_INPUTS@
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19 bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}'
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20 ]]>
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21 </command>
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23 <inputs>
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24 <expand macro="bam_sam_param" />
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25 <expand macro="mapq_param" />
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26 </inputs>
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27
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28 <outputs>
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29 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/>
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30 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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35 <output name="output" file="output.bamstats.txt" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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36 </test>
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37 </tests>
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39 <help><![CDATA[
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40 bam_stat.py
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41 +++++++++++
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42
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43 This program is used to calculate reads mapping statistics from provided BAM
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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44 file. This script determines "uniquely mapped reads" from `mapping quality
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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45 <http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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46 which quality the probability that a read is misplaced (Do NOT confused with
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47 sequence quality, sequence quality measures the probability that a base-calling
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48 was wrong) .
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50 Inputs
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51 ++++++++++++++
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53 Input BAM/SAM file
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54 Alignment file in BAM/SAM format.
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56 Minimum mapping quality
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57 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
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58
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59 Output
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60 ++++++++++++++
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61
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62 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
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63 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
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64 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
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65 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
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66
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67 @ABOUT@
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69 ]]>
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70 </help>
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72 <expand macro="citations" />
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73 </tool>