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annotate bam_stat.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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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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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <version_command><![CDATA[bam_stat.py --version]]></version_command>
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12 <command><![CDATA[
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13 @BAM_SAM_INPUTS@
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14 bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="bam_sam_param"/>
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19 <expand macro="mapq_param"/>
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20 </inputs>
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21 <outputs>
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22 <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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27 <output name="output" file="output.bamstats.txt"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 bam_stat.py
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32 +++++++++++
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33
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34 This program is used to calculate reads mapping statistics from provided BAM
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35 file. This script determines "uniquely mapped reads" from `mapping quality
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36 <http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
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37 which quality the probability that a read is misplaced (Do NOT confused with
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38 sequence quality, sequence quality measures the probability that a base-calling
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39 was wrong) .
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40
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41 Inputs
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42 ++++++++++++++
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43
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44 Input BAM/SAM file
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45 Alignment file in BAM/SAM format.
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47 Minimum mapping quality
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48 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
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50 Output
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51 ++++++++++++++
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52
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53 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
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54 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
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55 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
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56 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
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58 @ABOUT@
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60 ]]>
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61 </help>
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62 <expand macro="citations"/>
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63 </tool>