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annotate slamdunk.xml @ 3:24657d5edede 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 16:47:01 -0500
parents fae4a5ec0653
children 8b62f89924a7
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fae4a5ec0653 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>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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4 <import>macros.xml</import>
57bf9a0d49a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
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5 </macros>
57bf9a0d49a5 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>
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8 <command detect_errors="exit_code"><![CDATA[
2
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9 #import re
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fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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11 #if $reference_source.reference_source_selector == 'history':
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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12 ln -f -s '$reference_source.ref_file' reference.fa &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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13 #else:
fae4a5ec0653 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 &&
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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15 #end if
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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16
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17 mkdir ./fastq &&
fae4a5ec0653 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:
fae4a5ec0653 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))
fae4a5ec0653 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}' &&
fae4a5ec0653 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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fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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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
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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26 $multimapper.multimap
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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27 #if $multimapper.filterbed.bedtofilter:
fae4a5ec0653 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
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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29 #end if
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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30 -5 $quantseq.trim5
fae4a5ec0653 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
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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34 -mi $advanced.minID
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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35 -nm=$advanced.maxNM
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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36 -mc $advanced.minCov
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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37 -mv $advanced.minVar
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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38 -mbq $advanced.minBaseQual
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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39 -rl $readLength
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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40 -c $covThresh
fae4a5ec0653 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>
3fd7458bc861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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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"
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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"
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54 label="Maximum number of alignments to report per read"
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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=""
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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"
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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)." />
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84 <param name="minVar" type="float" min="0" value="0.8"
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85 label="Minimum variant fraction to call variant"
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86 help="Minimum variant fraction to call variant (default: 0.8)." />
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87 <param name="minBaseQual" type="integer" min="0" value="27"
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88 label="Minimum base quality"
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89 help="Minimum base quality for T>C conversions (default: 27)." />
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90 </section>
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91 <param name="covThresh" type="integer" min="1" value="1"
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92 label="T>C conversion threshold"
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93 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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94 <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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95 label="Read length"
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96 help="Maximum read length (before trimming)." />
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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 ${on_string}: BAM">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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100 <discover_datasets pattern="(?P&lt;name&gt;.+)\.bam$" format="bam" directory="./out/filter" visible="false" />
fae4a5ec0653 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 ${on_string}: Count TSV">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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103 <discover_datasets pattern="(?P&lt;name&gt;.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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104 </collection>
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105 <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF">
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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106 <discover_datasets pattern="(?P&lt;name&gt;.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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107 </collection>
0
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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
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112 <param name="reference_source_selector" value="history" />
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113 <param name="ref_file" value="ref.fa" />
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114 <param name="Reference" value="actb.bed" />
2
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115 <param name="reads" value="reads.fq" />
0
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116 <param name="readLength" value="100" />
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117 <section name="quantseq">
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118 <param name="trim5" value="0" />
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119 </section>
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120 <section name="advanced">
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121 <param name="minBaseQual" value="27" />
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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" />
fae4a5ec0653 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"
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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128 lines_diff="2" />
fae4a5ec0653 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">
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131 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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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" />
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137 <param name="Reference" value="actb.bed" />
2
fae4a5ec0653 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
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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" />
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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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"
fae4a5ec0653 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
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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.
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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>