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annotate slamdunk.xml @ 0:3fd7458bc861 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 20:33:07 -0400
parents
children 57bf9a0d49a5
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3fd7458bc861 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">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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3 <requirements>
3fd7458bc861 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>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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5 </requirements>
3fd7458bc861 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>
3fd7458bc861 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[
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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8 #if $reference_source.reference_source_selector == 'history':
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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9 ln -f -s '$reference_source.ref_file' reference.fa &&
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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10 #else:
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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11 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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12 #end if
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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13 slamdunk all -r reference.fa -b '$Reference' -o ./out
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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14 -n $multimapper.multimappers
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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15 $multimapper.multimap
3fd7458bc861 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:
3fd7458bc861 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
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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18 #end if
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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19 -5 $quantseq.trim5
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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20 -a $quantseq.maxpolyA
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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21 $advanced.endtoend
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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22 -mq $advanced.minMQ
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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23 -mi $advanced.minID
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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24 -nm=$advanced.maxNM
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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25 -mc $advanced.minCov
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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26 -mv $advanced.minVar
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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27 -mbq $advanced.minBaseQual
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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28 -rl $readLength
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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29 -c $covThresh
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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30 '$Reads'
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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31 ]]></command>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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32 <inputs>
3fd7458bc861 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">
3fd7458bc861 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">
3fd7458bc861 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>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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36 <option value="history">Use a FASTA from history</option>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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37 </param>
3fd7458bc861 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">
3fd7458bc861 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">
3fd7458bc861 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">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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41 <filter type="sort_by" column="2" />
3fd7458bc861 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" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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43 </options>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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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"/>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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45 </param>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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46 </when>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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47 <when value="history">
3fd7458bc861 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" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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49 </when>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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50 </conditional>
3fd7458bc861 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" />
3fd7458bc861 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" />
3fd7458bc861 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"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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54 expanded="false">
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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55 <section name="filterbed"
3fd7458bc861 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">
3fd7458bc861 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"
3fd7458bc861 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" />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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59 </section>
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 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." />
3fd7458bc861 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=""
3fd7458bc861 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."
3fd7458bc861 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." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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66 </section>
3fd7458bc861 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">
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 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." />
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 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." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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74 </section>
3fd7458bc861 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">
3fd7458bc861 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=""
3fd7458bc861 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."
3fd7458bc861 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" />
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 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)." />
3fd7458bc861 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"
3fd7458bc861 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)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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84 <param name="minID" type="float" min="0" value="0.95"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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85 label="Minimum alignment identity"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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86 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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87 <param name="maxNM" type="integer" value="-1"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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88 label="Maximum number of mismatches"
3fd7458bc861 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)." />
3fd7458bc861 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"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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91 label="Minimum coverage to call variant"
3fd7458bc861 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)." />
3fd7458bc861 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"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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94 label="Minimum variant fraction to call variant"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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95 help="Minimum variant fraction to call variant (default: 0.8)." />
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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98 help="Minimum base quality for T>C conversions (default: 27)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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99 </section>
3fd7458bc861 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"
3fd7458bc861 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"
3fd7458bc861 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)." />
3fd7458bc861 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"
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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104 label="Read length"
3fd7458bc861 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)." />
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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106 </inputs>
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107 <outputs>
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108 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" />
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109 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" />
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110 </outputs>
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111 <tests>
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112 <test>
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113 <param name="reference_source_selector" value="history" />
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114 <param name="ref_file" value="ref.fa" />
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115 <param name="Reference" value="actb.bed" />
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116 <param name="Reads" value="reads.fq" />
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117 <param name="readLength" value="100" />
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118 <section name="quantseq">
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119 <param name="trim5" value="0" />
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120 </section>
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121 <section name="advanced">
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122 <param name="minBaseQual" value="27" />
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123 </section>
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124 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
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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" />
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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" />
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132 <param name="readLength" value="100" />
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133 <section name="quantseq">
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134 <param name="trim5" value="0" />
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135 </section>
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136 <section name="advanced">
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137 <param name="minBaseQual" value="27" />
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138 </section>
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139 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv"
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140 lines_diff="2" />
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141 </test>
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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 ========
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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.
3fd7458bc861 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>`_
3fd7458bc861 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 ========
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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.
3fd7458bc861 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
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158 =============== ==========================================================================================================================================================
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159 **Genome** The reference fasta file (Genome assembly).
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160 **Reference** BED-file containing coordinates for 3' UTRs.
3fd7458bc861 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).
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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:
3fd7458bc861 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
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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
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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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>