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annotate slamdunk.xml @ 0:a4de8b7d6f10 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
author iuc
date Thu, 11 Oct 2018 20:32:45 -0400
parents
children 9dfecde9fa06
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0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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1 <tool id="slamdunk" name="Slamdunk" version="0.3.3">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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3 <requirements>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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4 <requirement type="package" version="0.3.3">slamdunk</requirement>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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5 </requirements>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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6 <version_command>slamdunk --version</version_command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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7 <command detect_errors="exit_code"><![CDATA[
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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8 #if $reference_source.reference_source_selector == 'history':
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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9 ln -f -s '$reference_source.ref_file' reference.fa &&
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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10 #else:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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11 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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12 #end if
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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13 slamdunk all -r reference.fa -b '$Reference' -o ./out
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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14 -n $multimapper.multimappers
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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15 $multimapper.multimap
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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16 #if $multimapper.filterbed.bedtofilter:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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17 -fb $multimapper.filterbed.bedtofilter
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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18 #end if
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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19 -5 $quantseq.trim5
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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20 -a $quantseq.maxpolyA
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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21 $advanced.endtoend
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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22 -mq $advanced.minMQ
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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23 -mi $advanced.minID
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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24 -nm=$advanced.maxNM
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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25 -mc $advanced.minCov
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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26 -mv $advanced.minVar
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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27 -mbq $advanced.minBaseQual
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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28 -rl $readLength
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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29 -c $covThresh
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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30 '$Reads'
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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31 ]]></command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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32 <inputs>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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33 <conditional name="reference_source">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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34 <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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35 <option value="cached">Use a built-in FASTA</option>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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36 <option value="history">Use a FASTA from history</option>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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37 </param>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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38 <when value="cached">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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39 <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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40 <options from_data_table="all_fasta">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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41 <filter type="sort_by" column="2" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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42 <validator type="no_options" message="No reference genomes are available" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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43 </options>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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45 </param>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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46 </when>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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47 <when value="history">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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48 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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49 </when>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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50 </conditional>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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51 <param name="Reference" type="data" format="bed" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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52 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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53 <section name="multimapper" title="Multimapper recovery"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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54 expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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55 <section name="filterbed"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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56 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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57 <param name="bedtofilter" type="data" format="bed" optional="true"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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58 label="Bed to filter" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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59 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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60 <param name="multimappers" type="integer" min="1" value="1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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61 label="Maximum number of alignments to report per read"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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62 help="The maximum number of alignments is used to track multimapping read alignments. The more are allowed, the more sensitive the multimapper filtering will be, but also the longer the runtime will be. 100 was used in previous publications." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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63 <param name="multimap" type="boolean" truevalue="--multimap" falsevalue=""
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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64 label="Use reference bed file to resolve multimappers."
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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65 help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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66 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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67 <section name="quantseq" title="Quantseq" expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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68 <param name="trim5" type="integer" min="0" value="12"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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69 label="Number of bp to remove from the 5' end of all reads"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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70 help="For Lexogen's Quantseq kit and previous SLAM-seq papers a clipping of 12 bp from the 5' end is recommended." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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71 <param name="maxpolyA" type="integer" min="0" value="4"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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72 label="Maximum number of As at the 3' end of a read"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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73 help="The maximum number of allowed As at the 3' end of a read. All A-stretches that exceed this threshold are clipped because they are likely part of the poly-A tail." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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74 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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75 <section name="advanced" title="Advanced settings." expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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76 <param name="endtoend" type="boolean" truevalue="--endtoend" falsevalue=""
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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77 label="Enable end-to-end alignments for mapping."
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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78 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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79 <param name="minMQ" type="integer" min="0" value="2"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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80 label="Minimum mapping quality"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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81 help="Minimum mapping quality to consider alignments (default: 2)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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82 <param name="minMQ" type="integer" label="Minimum mapping quality" min="0" value="2"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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83 help="Minimum mapping quality to consider alignments (default: 2)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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diff changeset
84 <param name="minID" type="float" min="0" value="0.95"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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diff changeset
85 label="Minimum alignment identity"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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diff changeset
86 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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87 <param name="maxNM" type="integer" value="-1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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88 label="Maximum number of mismatches"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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89 help="Maximum number of mismatches to consider alignments. Negative numbers deactivate filter (default: -1)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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90 <param name="minCov" type="integer" min="0" value="10"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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91 label="Minimum coverage to call variant"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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92 help="Minimum coverage to call variant (default: 10)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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93 <param name="minVar" type="float" min="0" value="0.8"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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94 label="Minimum variant fraction to call variant"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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diff changeset
95 help="Minimum variant fraction to call variant (default: 0.8)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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96 <param name="minBaseQual" type="integer" min="0" value="27"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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97 label="Minimum base quality"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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98 help="Minimum base quality for T>C conversions (default: 27)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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99 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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100 <param name="covThresh" type="integer" min="1" value="1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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101 label="T>C conversion threshold"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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102 help="Number of T>C conversions required to count a read as a T>C read (default: 1)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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103 <param name="readLength" type="integer" min="50" value="50"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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104 label="Read length"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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105 help="Maximum read length (before trimming)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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106 </inputs>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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107 <outputs>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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108 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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109 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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110 </outputs>
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111 <tests>
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112 <test>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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113 <param name="reference_source_selector" value="history" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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114 <param name="ref_file" value="ref.fa" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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115 <param name="Reference" value="actb.bed" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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116 <param name="Reads" value="reads.fq" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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117 <param name="readLength" value="100" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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118 <section name="quantseq">
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119 <param name="trim5" value="0" />
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120 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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121 <section name="advanced">
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122 <param name="minBaseQual" value="27" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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123 </section>
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124 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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125 lines_diff="2" />
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126 </test>
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127 <test>
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128 <!-- test built-in fasta -->
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129 <param name="reference_source_selector" value="cached" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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130 <param name="Reference" value="actb.bed" />
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131 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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132 <param name="readLength" value="100" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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133 <section name="quantseq">
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134 <param name="trim5" value="0" />
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135 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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136 <section name="advanced">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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137 <param name="minBaseQual" value="27" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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138 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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139 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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140 lines_diff="2" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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141 </test>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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142 </tests>
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143 <help><![CDATA[
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144 SLAM-seq
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145 ========
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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146
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147 SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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148
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149 Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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150
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151 Slamdunk
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152 ========
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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153
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154 To analyze a given SLAM-seq dataset with *slamdunk* without recovering multimappers, you only need to provide the following files and keep everything else to the default parameters.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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155
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156 =============== ==========================================================================================================================================================
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157 Parameter Description
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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158 =============== ==========================================================================================================================================================
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159 **Genome** The reference fasta file (Genome assembly).
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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160 **Reference** BED-file containing coordinates for 3' UTRs.
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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161 **Reads** Sample FASTQ(gz) files.
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162 **Read length** Maximum length of reads (usually 50, 100, 150).
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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163 =============== ==========================================================================================================================================================
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164
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165 This will run the entire *slamdunk* analysis with the most relevant output files being:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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166
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167 * Tab-separated *tcount* file containing the SLAM-seq statistics per UTR
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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168 * BAM-file with the final mapped reads for visualization and further processing
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169
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170 ------------------------------------------------------
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171
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172 Multimapper recovery
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173 --------------------
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174
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175 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
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176 on the supplied reference file. Will only yield different results than a unique-mapping run by specifying a number > 1 as maximum number of multimapper aligments to consider.
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177
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178 =================================================== =========================================================
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179 Parameter Description
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180 =================================================== =========================================================
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181 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
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182 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
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183 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
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184 =================================================== =========================================================
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185
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186 ------------------------------------------------------
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187
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188 T>C conversions
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189 ---------------
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190
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191 Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 <http://science.sciencemag.org/content/early/2018/04/04/science.aao2793>`_
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192
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193 This can be controlled by the following parameter:
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194
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195 ============================ ================================================================================
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196 Parameter Description
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197 ============================ ================================================================================
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198 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
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199 ============================ ================================================================================
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200
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201
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202 ]]></help>
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203 <citations>
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204 <citation type="bibtex">
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205 @misc{Neumann2018,
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206 author = {Neumann, Tobias},
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207 year = {2018},
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208 title = Slamdunk},
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209 publisher = {GitHub},
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210 journal = {GitHub repository},
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211 url = {https://github.com/t-neumann/slamdunk},
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212 }
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213 </citation>
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214 </citations>
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215 </tool>