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annotate slamdunk.xml @ 3:17f54c2f4b0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 11770937d250d7a332875becf06b9a42b17c46d1
author iuc
date Mon, 21 Jan 2019 16:46:31 -0500
parents 4b677ea9314a
children 40291a9a9c37
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4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy2">
0
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2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
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6 <expand macro="requirements" />
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7 <version_command>slamdunk --version</version_command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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8 <command detect_errors="exit_code"><![CDATA[
2
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9 #import re
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10
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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11 #if $reference_source.reference_source_selector == 'history':
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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12 ln -f -s '$reference_source.ref_file' reference.fa &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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13 #else:
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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15 #end if
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16
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17 mkdir ./fastq &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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18 #for $fastq in $reads:
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier))
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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20 ln -s '$fastq' './fastq/${fastq_name}' &&
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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21 #end for
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23 slamdunk all -r reference.fa -b '$Reference' -o ./out
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24 -t \${GALAXY_SLOTS:-1}
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25 -n $multimapper.multimappers
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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26 $multimapper.multimap
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27 #if $multimapper.filterbed.bedtofilter:
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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28 -fb $multimapper.filterbed.bedtofilter
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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29 #end if
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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30 -5 $quantseq.trim5
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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31 -a $quantseq.maxpolyA
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32 $advanced.endtoend
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33 -mq $advanced.minMQ
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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34 -mi $advanced.minID
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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35 -nm=$advanced.maxNM
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36 -mc $advanced.minCov
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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37 -mv $advanced.minVar
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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38 -mbq $advanced.minBaseQual
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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39 -rl $readLength
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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40 -c $covThresh
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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41 ./fastq/*
0
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42 ]]></command>
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43 <inputs>
1
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44 <expand macro="reference_files" />
2
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45 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="True" label="FASTQ files"/>
0
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46 <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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47 expanded="false">
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48 <section name="filterbed"
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49 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
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50 <param name="bedtofilter" type="data" format="bed" optional="true"
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51 label="Bed to filter" />
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52 </section>
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53 <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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54 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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55 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." />
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56 <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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57 label="Use reference bed file to resolve multimappers."
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58 help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />
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59 </section>
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60 <section name="quantseq" title="Quantseq" expanded="false">
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61 <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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62 label="Number of bp to remove from the 5' end of all reads"
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63 help="For Lexogen's Quantseq kit and previous SLAM-seq papers a clipping of 12 bp from the 5' end is recommended." />
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64 <param name="maxpolyA" type="integer" min="0" value="4"
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65 label="Maximum number of As at the 3' end of a read"
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66 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." />
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67 </section>
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68 <section name="advanced" title="Advanced settings." expanded="false">
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69 <param name="endtoend" type="boolean" truevalue="--endtoend" falsevalue=""
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70 label="Enable end-to-end alignments for mapping."
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71 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
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72 <param name="minMQ" type="integer" min="0" value="2"
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73 label="Minimum mapping quality"
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74 help="Minimum mapping quality to consider alignments (default: 2)." />
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75 <param name="minID" type="float" min="0" value="0.95"
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76 label="Minimum alignment identity"
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77 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
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78 <param name="maxNM" type="integer" value="-1"
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79 label="Maximum number of mismatches"
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80 help="Maximum number of mismatches to consider alignments. Negative numbers deactivate filter (default: -1)." />
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81 <param name="minCov" type="integer" min="0" value="10"
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82 label="Minimum coverage to call variant"
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83 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
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84 <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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85 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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86 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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87 <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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88 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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89 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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90 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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91 <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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92 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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93 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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94 <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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95 label="Read length"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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96 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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97 </inputs>
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98 <outputs>
2
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99 <collection name="outputBam" type="list" label="${tool.name} on ${on_string}: BAM">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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100 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bam$" format="bam" directory="./out/filter" visible="false" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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101 </collection>
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102 <collection name="outputTsv" type="list" label="${tool.name} on ${on_string}: Count TSV">
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103 <discover_datasets pattern="(?P&lt;name&gt;.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" />
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104 </collection>
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105 <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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106 <discover_datasets pattern="(?P&lt;name&gt;.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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107 </collection>
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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108 </outputs>
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109 <tests>
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110 <test>
1
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111 <!--Ensure default outputs work -->
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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112 <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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113 <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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114 <param name="Reference" value="actb.bed" />
2
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115 <param name="reads" value="reads.fq" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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116 <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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117 <section name="quantseq">
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118 <param name="trim5" value="0" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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119 </section>
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120 <section name="advanced">
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121 <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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122 </section>
2
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123 <output_collection name="outputBam">
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124 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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125 </output_collection>
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126 <output_collection name="outputTsv">
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127 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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128 lines_diff="2" />
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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129 </output_collection>
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130 <output_collection name="outputVcf">
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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131 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
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132 </output_collection>
0
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133 </test>
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134 <test>
1
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135 <!--Ensure built-in fasta works -->
0
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136 <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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137 <param name="Reference" value="actb.bed" />
2
4b677ea9314a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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138 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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139 <param name="readLength" value="100" />
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140 <section name="quantseq">
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141 <param name="trim5" value="0" />
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142 </section>
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143 <section name="advanced">
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144 <param name="minBaseQual" value="27" />
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145 </section>
2
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146 <output_collection name="outputBam">
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147 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" />
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148 </output_collection>
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149 <output_collection name="outputTsv">
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150 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
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151 lines_diff="2" />
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152 </output_collection>
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153 <output_collection name="outputVcf">
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154 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
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155 </output_collection>
0
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156 </test>
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157 </tests>
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158 <help><![CDATA[
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159 SLAM-seq
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160 ========
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161
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162 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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163
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164 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>`_
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165
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166 Slamdunk
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167 ========
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168
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169 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.
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170
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171 =============== ==========================================================================================================================================================
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172 Parameter Description
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173 =============== ==========================================================================================================================================================
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174 **Genome** The reference fasta file (Genome assembly).
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175 **Reference** BED-file containing coordinates for 3' UTRs.
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176 **Reads** Sample FASTQ(gz) files.
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177 **Read length** Maximum length of reads (usually 50, 100, 150).
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178 =============== ==========================================================================================================================================================
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179
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180 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
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181
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182 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
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183 * BAM-file with the final filtered mapped reads
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184 * VCF file of variants called on the final filtered alignments
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185
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186 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
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187
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188 ------------------------------------------------------
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189
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190 Multimapper recovery
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191 --------------------
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192
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193 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
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194 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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195
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196 =================================================== =========================================================
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197 Parameter Description
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198 =================================================== =========================================================
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199 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
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200 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
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201 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
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202 =================================================== =========================================================
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203
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204 ------------------------------------------------------
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205
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206 T>C conversions
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207 ---------------
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208
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209 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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210
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211 This can be controlled by the following parameter:
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212
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213 ============================ ================================================================================
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214 Parameter Description
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215 ============================ ================================================================================
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216 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
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217 ============================ ================================================================================
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218
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219 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
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220
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221 ]]></help>
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222 <citations>
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223 <expand macro="citations" />
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224 </citations>
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225 </tool>