Mercurial > repos > jdv > b2b_count_mapped_reads

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:11:32 +0000
parents 6fb0eff46972
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6fb0eff46972 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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1 <tool id="b2b_count_mapped_reads" name="Count mapped reads" version="0.001">
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3 <description>Count reads uniquely mapped to each reference sequence</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
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9 <requirement type="package" version="6.1">ncurses</requirement>
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10 <requirement type="package" version="1.9">samtools</requirement>
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11 </requirements>
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6fb0eff46972 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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13 <!-- ***************************************************************** -->
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15 <version_command>echo "0.001"</version_command>
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17 <!-- ***************************************************************** -->
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19 <command detect_errors="aggressive">
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20 <![CDATA[
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22 #if $uniq:
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23 samtools view -F 0x04 -F 0x100 -F 0x800 $in
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24 #else
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25 samtools view -F 0x04 $in
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26 #end if
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27 | cut -f3
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28 | sort
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29 | uniq -c
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30 | awk -v OFS='\t' '{print $2,$1}'
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31 > $out
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33 ]]>
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34 </command>
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36 <!-- ***************************************************************** -->
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38 <inputs>
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39 <param name="in" type="data" format="bam" label="Read mapping" help="BAM format" />
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40 <param name="uniq" type="boolean" checked="True" label="Exclude ambiguous mappings" />
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41 </inputs>
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43 <!-- ***************************************************************** -->
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45 <outputs>
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46 <data name="out" format="tabular" label="Read counts" />
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47 </outputs>
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49 <!-- ***************************************************************** -->
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51 <tests>
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52 <test>
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53 <param name="in" value="b2c.bam" ftype="bam" />
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54 <output name="out" file="b2c.counts" compare="diff" />
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55 </test>
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56 </tests>
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58 <!-- ***************************************************************** -->
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60 <help>
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62 `count_mapped_reads` is a Galaxy-only utility from BASE2BIO that simply
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63 reports the number of reads mapped to each sequence from a BAM input file.
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65 </help>
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67 <!-- ***************************************************************** -->
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69 <citations>
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70 </citations>
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72 </tool>