Mercurial > repos > lparsons > rseqc

annotate bam_stat.xml @ 1:cd2daa987b69 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
author lparsons
date Tue, 07 Jul 2015 14:14:04 -0400
parents 306127635959
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306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4galaxy1">
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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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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <requirements>
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11 <expand macro="requirement_package_numpy" />
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12 <expand macro="requirement_package_rseqc" />
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13 </requirements>
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15 <expand macro="stdio" />
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17 <version_command><![CDATA[bam_stat.py --version]]></version_command>
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19 <command><![CDATA[
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20 bam_stat.py -i $input -q $mapq 2> $output
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21 ]]>
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22 </command>
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24 <inputs>
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25 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
cd2daa987b69 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
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26 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
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27 </inputs>
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29 <outputs>
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30 <data format="txt" name="output" />
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31 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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36 <output name="output" file="bamstats.txt"/>
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37 </test>
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38 </tests>
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40 <help><![CDATA[
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41 bam_stat.py
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42 +++++++++++
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44 This program is used to calculate reads mapping statistics from provided BAM
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45 file. This script determines "uniquely mapped reads" from `mapping quality
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46 <http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
0
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47 which quality the probability that a read is misplaced (Do NOT confused with
306127635959 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit aeb25d807817746dd6957f30ce2070662cc10e91
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48 sequence quality, sequence quality measures the probability that a base-calling
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49 was wrong) .
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51 Inputs
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52 ++++++++++++++
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54 Input BAM/SAM file
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55 Alignment file in BAM/SAM format.
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57 Minimum mapping quality
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58 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
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60 Output
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61 ++++++++++++++
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63 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
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64 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
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65 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
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66 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
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68 -----
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70 About RSeQC
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71 +++++++++++
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74 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
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76 The RSeQC package is licensed under the GNU GPL v3 license.
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78 .. image:: http://rseqc.sourceforge.net/_static/logo.png
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80 .. _RSeQC: http://rseqc.sourceforge.net/
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82 ]]>
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83 </help>
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85 <expand macro="citations" />
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86 </tool>