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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
author artbio
date Wed, 15 Jun 2022 15:37:11 +0000
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7883d97fa479 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
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1 <tool id="mapqstatistics" name="Mapping Quality Stats" version="0.19.1+galaxy0">
0
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2 <description></description>
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3 <requirements>
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7883d97fa479 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
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4 <requirement type="package" version="1.7.1">r-optparse</requirement>
7883d97fa479 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
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5 <requirement type="package" version="3.3.6">r-ggplot2</requirement>
7883d97fa479 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit 73d041253a6c8d3f1126894c547e43dda5e700c1
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6 <requirement type="package" version="0.19.1">pysam</requirement>
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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7 </requirements>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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8 <stdio>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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10 </stdio>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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11 <command detect_errors="exit_code"><![CDATA[
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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12 ln -f -s $input.metadata.bam_index input.bam.bai &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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13 ln -s $input input.bam &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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14 python $__tool_directory__/mapping_quality_stats.py
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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15 -bam input.bam
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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16 -o $table &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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17 Rscript $__tool_directory__/mapping_quality_stats.r
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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18 -i '$table'
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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19 -o $plot
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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20 ]]></command>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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21 <inputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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22 <param name="input" type="data" format="bam" label="Select a bam file to analyze"/>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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23 </inputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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25 <outputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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26 <data format="tabular" name="table" label="Distribution table" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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27 <data format="pdf" name="plot" label="Distribution of MAPQs" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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28 </outputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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30 <tests>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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31 <test>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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32 <param name="input" value="sample.bam" ftype="bam"/>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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33 <output file="distribution.tab" name="table" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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34 <output file="distribution.pdf" name="plot" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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35 </test>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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36 </tests>
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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39 <help>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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41 **What it does**
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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43 Collects the values of mapping quality (MAPQ) in a BAM files
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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44 Shows the data as a table and a barplot
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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46 **Inputs**
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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48 A bam alignment files which must be sorted
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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50 **Output**
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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52 A data frame of MAPQ counts
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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54 A pdf barplot generated by R and ggplot2
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f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
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56 </help>
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58 <citations>
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59 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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60 </citations>
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61 </tool>
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