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annotate bam_stat.xml @ 4:caaa120457bc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7f68686cac77df831f1a26a2126a238a2e480316
author iuc
date Tue, 21 Nov 2017 14:55:14 -0500
parents 71ed55a3515a
children d7f6b3653d84
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71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@WRAPPER_VERSION@">
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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2 <description>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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3 reads mapping statistics for a provided BAM or SAM file.
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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4 </description>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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6 <macros>
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7 <import>rseqc_macros.xml</import>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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8 </macros>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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10 <expand macro="requirements" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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12 <expand macro="stdio" />
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71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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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_stat.py -i '${input}' -q ${mapq} > '${output}'
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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18 ]]>
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19 </command>
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21 <inputs>
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22 <expand macro="bam_param" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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23 <expand macro="mapq_param" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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24 </inputs>
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26 <outputs>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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27 <data format="txt" name="output" />
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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28 </outputs>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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30 <tests>
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31 <test>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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32 <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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33 <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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34 </test>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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35 </tests>
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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37 <help><![CDATA[
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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38 bam_stat.py
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39 +++++++++++
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41 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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42 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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43 <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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44 which quality the probability that a read is misplaced (Do NOT confused with
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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45 sequence quality, sequence quality measures the probability that a base-calling
71ed55a3515a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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46 was wrong) .
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48 Inputs
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49 ++++++++++++++
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51 Input BAM/SAM file
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52 Alignment file in BAM/SAM format.
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54 Minimum mapping quality
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55 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
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56
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57 Output
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58 ++++++++++++++
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59
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60 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
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61 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
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62 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
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63 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
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64
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65 @ABOUT@
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67 ]]>
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68 </help>
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70 <expand macro="citations" />
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71 </tool>