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annotate instrain_profile.xml @ 0:1f3730540302 draft

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"planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
author iuc
date Wed, 11 Aug 2021 21:11:18 +0000
parents
children c332659ecdcc
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0
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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1 <tool id="instrain_profile" name="InStrain Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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2 <description>Creates an inStrain profile (microdiversity analysis) from a mapping file </description>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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3 <macros>
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4 <import>macros.xml</import>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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5 </macros>
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6 <expand macro="edam_ontology"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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7 <expand macro="requirements">
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8 <requirement type="package" version="3.0">zip</requirement>
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9 </expand>
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10 <version_command>inStrain profile --version</version_command>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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11 <command detect_errors="exit_code"><![CDATA[
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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12 #set ext=$mapping_input.datatype.file_ext
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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13 ln -s '$mapping_input' 'inputbam.$ext'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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14 #if $gene_profiling.gene_file
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15 &&
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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16 ln -s '$gene_profiling.gene_file' 'gene_file.fna'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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17 #end if
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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18 #if $stb
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19 &&
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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20 ln -s '$stb' 'stb_file.stb'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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21 #end if
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22 &&
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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23 inStrain profile
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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24 'inputbam.$ext'
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25 '$sequence_input'
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26 --output 'inStrain.IS'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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27 $use_full_fasta_header
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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28 --processes "\${GALAXY_SLOTS:-6}"
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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29 --min_mapq $read_filtering.min_mapq
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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30 --max_insert_relative $read_filtering.max_insert_relative
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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31 --min_insert $read_filtering.min_insert
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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32 --pairing_filter '$read_filtering.pairing_filter'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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33 #if $priority_reads
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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34 --priority_reads '$read_filtering.priority_reads'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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35 #end if
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36 $output.detailed_mapping_info
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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37 --min_cov $variant_calling.min_cov
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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38 --min_freq $variant_calling.min_freq
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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39 --fdr $variant_calling.fdr
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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40 #if $gene_file
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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41 --gene_file 'gene_file.fna'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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42 #end if
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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43 #if $stb
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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44 --stb 'stb_file.stb'
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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45 #end if
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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46 $mm_level
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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47 #if $profile.database_mode
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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48 $profile.database_mode
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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49 #else
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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50 --min_read_ani $read_filtering.min_read_ani
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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51 --min_genome_coverage $profile.min_genome_coverage
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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52 $skip_mm_profiling
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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53 #end if
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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54 --min_scaffold_reads $profile.min_scaffold_reads
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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55 --min_snp $profile.min_snp
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56 $profile.store_everything
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57 #if $profile.scaffolds_to_profile
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58 --scaffolds_to_profile '$profile.scaffolds_to_profile'
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59 #end if
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60 --rarefied_coverage $profile.rarefied_coverage
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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61 --window_length $profile.window_length
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62 $output.skip_genome_wide
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63 $output.skip_plot_generation
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64 &&
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65 cd ./inStrain.IS && zip -r ../inStrain.IS.zip *
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66 ]]></command>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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67 <inputs>
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68 <param name="mapping_input" type="data" format="bam,sam" label="A file containing metagenomic reads mapped to a DNA sequence" help="Sorted Bam file"/>
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69 <param name="sequence_input" type="data" format="fasta" label="A file containing a DNA sequence."/>
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70 <param argument="--use_full_fasta_header" type="boolean" truevalue="--use_full_fasta_header" falsevalue="" checked="false" label="Use full fasta header" help="Instead of using the fasta ID (space in header before space), use the full header. Needed for some mapping tools (including bbMap)"/>
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71 <section name="read_filtering" title="Read Filtering" expanded="true">
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72 <param argument="--min_read_ani" type="float" value="0.95" min="0" max="1" label="Minimum percent identity" help=" Minimum percent identity of read pairs to consensus to use the reads. Must be >, not >="/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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73 <param argument="--min_mapq" type="integer" value="-1" label="Minimum mapq score" help="Minimum mapq score of EITHER read in a pair to use that pair. Must be >, not >="/>
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74 <param argument="--max_insert_relative" type="integer" value="3" label="Maximum insert relative" help="Multiplier to determine maximum insert size between two reads - default is to use 3x median insert size. Must be >, not >="/>
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75 <param argument="--min_insert" type="integer" value="50" label="Minimum insert" help="Minimum insert size between two reads - default is 50 bp. If two reads are 50bp each and overlap completely, their insert will be 50. Must be >, not >="/>
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76 <param argument="--pairing_filter" type="select" label="How should paired reads be handled?">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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77 <option value="paired_only" selected="true">Only paired reads are retained</option>
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78 <option value="non_discordant">Keep all paired reads and singleton reads that map to a single scaffold</option>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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79 <option value="all_reads">Keep all reads regardless of pairing status (NOT RECOMMENDED; See documentation for deatils)</option>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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80 </param>
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81 <param argument="--priority_reads" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="The location of a list of reads that should be retained regardless of pairing status" help="For example long reads or merged reads. This can be a .fastq file or text file with list of read names (will assume file is compressed if ends in .gz"/>
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82 </section>
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83 <section name="variant_calling" title="Variant Calling" expanded="true">
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84 <param argument="--min_cov" type="integer" value="5" label="Minimum coverage" help=" Minimum coverage to call a variant"/>
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85 <param argument="--min_freq" type="float" value="0.05" label="Minimum SNP frequency" help="Minimum SNP frequency to confirm a SNV (both this AND the FDR snp count cutoff must be true to call a SNP)."/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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86 <param argument="--fdr" type="float" value="1e-06" min="0" max="1" label="FDR" help="SNP false discovery rate- based on simulation data with a 0.1 percent error rate (Q30)"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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87 </section>
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88 <section name="gene_profiling" title="Gene Profiling" expanded="true">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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89 <param argument="--gene_file" type="data" format="fasta,genbank" optional="true" label="Path to prodigal .fna genes file. If file ends in .gb or .gbk, will treat as a genbank file" help="EXPERIMENTAL; the name of the gene must be in the gene qualifier"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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90 </section>
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91 <param argument="--stb" type="data" format="tabular" optional="true" label="Scaffold to bin" help="This can be a file with each line listing a scaffold and a bin name, tab-seperated. This can also be a space-seperated list of .fasta files, with one genome per .fasta file. If nothing is provided, all scaffolds will be treated as belonging to the same genome"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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92 <param argument="--mm_level" type="boolean" truevalue="--mm_level" falsevalue="" checked="false" label="Create output files on the mm level"/>
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93 <param argument="--skip_mm_profiling" type="boolean" truevalue="--skip_mm_profiling" falsevalue="" checked="false" label ="Skip mm profiling" help="Dont perform analysis on an mm level; saves RAM and time; impacts plots and raw_data"/>
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94 <section name="profile" title="Profile" expanded="true">
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95 <param argument="--database_mode" type="boolean" truevalue="--database_mode" falsevalue="" checked="false" label="Database mode" help="Set a number of parameters to values appropriate for mapping to a large fasta file."/>
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96 <param argument="--min_scaffold_reads" type="integer" value="1" label="Minimum scaffold reads" help="Minimum number of reads mapping to a scaffold to proceed with profiling it"/>
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97 <param argument="--min_genome_coverage" type="integer" value="0" label="Minimum genome coverage" help="Minimum number of reads mapping to a genome to proceed with profiling it. MUST profile .stb if this is set"/>
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98 <param argument="--min_snp" type="integer" value="20" label="Minimum SNP" help="Absolute minimum number of reads connecting two SNPs to calculate LD between them."/>
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99 <param argument="--store_everything" type="boolean" truevalue="--store_everything" falsevalue="" checked="false" label="Store everything" help="Store intermediate dictionaries in the pickle file; will result in significantly more RAM and disk usage"/>
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100 <param argument="--scaffolds_to_profile" type="data" format="fasta" optional="true" label="Scaffolds to profile" help="File containing a list of scaffolds to profile- if provided will ONLY profile those scaffolds"/>
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101 <param argument="--rarefied_coverage" type="integer" value="50" label="Rarefied coverage" help="When calculating nucleotide diversity, also calculate a rarefied version with this much coverage"/>
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102 <param argument="--window_length" type="integer" value="10000" label ="Window length" help="Break scaffolds into windows of this length when profiling"/>
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diff changeset
103 </section>
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104 <section name="output" title="Set Output Parameters" expanded="true">
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105 <param argument="--detailed_mapping_info" type="boolean" truevalue="--detailed_mapping_info" falsevalue="" checked="false" label="Detailed mapping info" help="Make a detailed read report indicating deatils about each individual mapped read"/>
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106 <param argument="--skip_genome_wide" type="boolean" truevalue="--skip_genome_wide" falsevalue="" checked="false" label="Skip genome wide" help="Do not generate tables that consider groups of scaffolds belonging to genomes"/>
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107 <param argument="--skip_plot_generation" type="boolean" truevalue="--skip_plot_generation" falsevalue="" checked="false" label="Skip plot generation" help="Do not make plots"/>
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108 </section>
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109 </inputs>
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110 <outputs>
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111 <data format="zip" name="inStrain_zip" from_work_dir="inStrain.IS.zip" label="inStrain Profile IS zip" />
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112 <data name="scaffold_info" format="tabular" from_work_dir="inStrain.IS/output/inStrain.IS_scaffold_info.tsv" label="Scoffold Info, This gives basic information about the scaffolds in your sample at the highest allowed level of read identity." />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
113 <data name="mapping_info" format="tabular" from_work_dir="inStrain.IS/output/inStrain.IS_mapping_info.tsv" label="Mapping Info, This provides an overview of the number of reads that map to each scaffold, and some basic metrics about their quality." />
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diff changeset
114 <data name="SNVs" format="tabular" from_work_dir="inStrain.IS/output/inStrain.IS_SNVs.tsv" label="SNV, This describes the SNVs and SNSs that are detected in this mapping." />
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diff changeset
115 <data format="tabular" name="linkage" from_work_dir="inStrain.IS/output/inStrain.IS_linkage.tsv" label="Linkage, This describes the linkage between pairs of SNPs in the mapping that are found on the same read pair at least min_snp times." />
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diff changeset
116 <data format="tabular" name="gene_info" from_work_dir="inStrain.IS/output/inStrain.IS_gene_info.tsv" label="Gene Info, This describes some basic information about the genes being profiled" />
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diff changeset
117 <data format="tabular" name="genome_info" from_work_dir="inStrain.IS/output/inStrain.IS_genome_info.tsv" label="Genome Info, This Describes many of the above metrics on a genome-by-genome level, rather than a scaffold-by-scaffold level." >
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diff changeset
118 <filter>(output['skip_genome_wide'] is False)</filter>
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diff changeset
119 </data>
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diff changeset
120 <collection name="figures_pdfs" type="list" label="Figures" >
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parents:
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121 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="inStrain.IS/figures/" format="pdf"/>
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122 <filter>(output['skip_plot_generation'] is False)</filter>
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diff changeset
123 </collection>
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parents:
diff changeset
124 </outputs>
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parents:
diff changeset
125 <tests>
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parents:
diff changeset
126 <test expect_num_outputs="6">
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127 <param name="mapping_input" value="SmallScaffold.fa.sorted.bam"/>
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diff changeset
128 <param name="sequence_input" value="SmallScaffold.fa"/>
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diff changeset
129 <param name="use_full_fasta_header" value="false"/>
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diff changeset
130 <param name="mm_level" value="false"/>
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parents:
diff changeset
131 <param name="skip_mm_profiling" value="false"/>
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diff changeset
132 <section name="read_filtering">
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diff changeset
133 <param name="min_read_ani" value="0.95"/>
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diff changeset
134 <param name="min_mapq" value="-1"/>
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diff changeset
135 <param name="max_insert_relative" value="3"/>
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parents:
diff changeset
136 <param name="min_insert" value="50"/>
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diff changeset
137 <param name="pairing_filter" value="paired_only"/>
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parents:
diff changeset
138 </section>
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parents:
diff changeset
139 <section name="variant_calling">
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140 <param name="min_cov" value="5"/>
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diff changeset
141 <param name="min_freq" value="0.05"/>
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diff changeset
142 <param name="fdr" value="1e-06"/>
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diff changeset
143 </section>
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parents:
diff changeset
144 <section name="profile">
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diff changeset
145 <param name="database_mode" value="false"/>
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diff changeset
146 <param name="min_scaffold_reads" value="1"/>
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diff changeset
147 <param name="min_genome_coverage" value="0"/>
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diff changeset
148 <param name="min_snp" value="20"/>
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diff changeset
149 <param name="store_everything" value="false"/>
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diff changeset
150 <param name="rarefied_coverage" value="50"/>
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parents:
diff changeset
151 <param name="window_length" value="10000"/>
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parents:
diff changeset
152 </section>
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parents:
diff changeset
153 <section name="output">
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154 <param name="detailed_mapping_info" value="false"/>
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diff changeset
155 <param name="skip_genome_wide" value="true"/>
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diff changeset
156 <param name="skip_plot_generation" value="true"/>
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parents:
diff changeset
157 </section>
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parents:
diff changeset
158 <output name="inStrain_zip">
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parents:
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159 <assert_contents>
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160 <has_size value="21606" delta="1000" />
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parents:
diff changeset
161 </assert_contents>
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diff changeset
162 </output>
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parents:
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163 <output name="scaffold_info">
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parents:
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164 <assert_contents>
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parents:
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165 <has_text text="length"/>
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parents:
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166 <has_n_lines n="2"/>
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parents:
diff changeset
167 <has_n_columns n="21"/>
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parents:
diff changeset
168 </assert_contents>
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diff changeset
169 </output>
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parents:
diff changeset
170 <output name="mapping_info">
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parents:
diff changeset
171 <assert_contents>
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parents:
diff changeset
172 <has_text text="scaffold"/>
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parents:
diff changeset
173 <has_n_lines n="5"/>
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parents:
diff changeset
174 </assert_contents>
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parents:
diff changeset
175 </output>
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parents:
diff changeset
176 <output name="SNVs">
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parents:
diff changeset
177 <assert_contents>
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parents:
diff changeset
178 <has_text text="position"/>
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parents:
diff changeset
179 <has_n_lines n="5"/>
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parents:
diff changeset
180 <has_n_columns n="16"/>
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parents:
diff changeset
181 </assert_contents>
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parents:
diff changeset
182 </output>
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parents:
diff changeset
183 <output name="linkage">
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diff changeset
184 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
185 <has_n_lines n="1"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
186 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
187 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
188 <output name="gene_info">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
189 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
190 <has_n_lines n="0"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
191 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
192 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
193 </test>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
194 <test expect_num_outputs="8">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
195 <param name="mapping_input" value="SmallScaffold.fa.sorted.bam"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
196 <param name="sequence_input" value="SmallScaffold.fa"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
197 <param name="use_full_fasta_header" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
198 <param name="mm_level" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
199 <param name="skip_mm_profiling" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
200 <section name="read_filtering">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
201 <param name="min_read_ani" value="0.95"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
202 <param name="min_mapq" value="-1"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
203 <param name="max_insert_relative" value="3"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
204 <param name="min_insert" value="50"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
205 <param name="pairing_filter" value="paired_only"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
206 </section>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
207 <section name="variant_calling">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
208 <param name="min_cov" value="5"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
209 <param name="min_freq" value="0.05"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
210 <param name="fdr" value="1e-06"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
211 </section>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
212 <section name="profile">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
213 <param name="database_mode" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
214 <param name="min_scaffold_reads" value="1"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
215 <param name="min_genome_coverage" value="0"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
216 <param name="min_snp" value="20"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
217 <param name="store_everything" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
218 <param name="rarefied_coverage" value="50"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
219 <param name="window_length" value="10000"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
220 </section>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
221 <section name="output">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
222 <param name="detailed_mapping_info" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
223 <param name="skip_genome_wide" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
224 <param name="skip_plot_generation" value="false"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
225 </section>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
226 <output name="inStrain_zip">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
227 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
228 <has_size value="1468006" delta="100000" />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
229 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
230 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
231 <output name="scaffold_info">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
232 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
233 <has_text text="length"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
234 <has_n_lines n="2"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
235 <has_n_columns n="21"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
236 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
237 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
238 <output name="mapping_info">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
239 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
240 <has_text text="scaffold"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
241 <has_n_lines n="5"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
242 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
243 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
244 <output name="SNVs">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
245 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
246 <has_text text="position"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
247 <has_n_lines n="5"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
248 <has_n_columns n="16"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
249 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
250 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
251 <output name="linkage">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
252 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
253 <has_n_lines n="1"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
254 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
255 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
256 <output name="gene_info">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
257 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
258 <has_n_lines n="0"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
259 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
260 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
261 <output name="genome_info">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
262 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
263 <has_text text="nucl_diversity"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
264 <has_n_lines n="2"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
265 <has_n_columns n="26"/>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
266 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
267 </output>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
268 <output_collection name="figures_pdfs" type="list">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
269 <element name="inStrain.IS_CoverageAndBreadth_vs_readMismatch.pdf" ftype="pdf">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
270 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
271 <has_size value="383078" delta="10000" />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
272 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
273 </element>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
274 <element name="inStrain.IS_MajorAllele_frequency_plot.pdf" ftype="pdf">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
275 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
276 <has_size value="383590" delta="10000" />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
277 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
278 </element>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
279 <element name="inStrain.IS_ReadFiltering_plot.pdf" ftype="pdf">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
280 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
281 <has_size value="383078" delta="10000" />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
282 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
283 </element>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
284 <element name="inStrain.IS_ScaffoldInspection_plot.pdf" ftype="pdf">
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
285 <assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
286 <has_size value="208" delta="10" />
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
287 </assert_contents>
1f3730540302 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
iuc
parents:
diff changeset
288 </element>
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289 <element name="inStrain.IS_genomeWide_microdiveristy_metrics.pdf" ftype="pdf">
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290 <assert_contents>
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291 <has_size value="208" delta="10" />
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292 </assert_contents>
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293 </element>
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294 <element name="inStrain.IS_readANI_distribution.pdf" ftype="pdf">
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295 <assert_contents>
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296 <has_size value="382771" delta="10000" />
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297 </assert_contents>
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298 </element>
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299 </output_collection>
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300 </test>
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301 </tests>
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302 <help><![CDATA[
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303 @HELP_HEADER@
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304
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305 Profile
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306 =======
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307
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308 is the heart of inStrain tool.
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309
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310 The functionality of inStrain profile is broken into several steps:
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311
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312 First, all reads in the .bam file are filtered to only keep those that map with sufficient quality. All non-paired reads will be filtered out by default, and an additional set of filters are applied to each read pair (not the individual reads):
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313
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314 - Pairs must be mapped in the proper orientation with an expected insert size. The minimum insert distance can be set with the tool's corresponding parameter. The maximum insert distance is a multiple of the median insert distance. So if pairs have a median insert size of 500bp, by default all pairs with insert sizes over 1500bp will be excluded. For the max insert cutoff, the median_insert for all scaffolds is used.
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315 - Pairs must have a minimum mapQ score. MapQ scores are confusing and how they’re calculated varies based on the mapping algorithm being used, but are meant to represent both the number of mismatches in the mapping and how unique that mapping is. With bowtie2, if the read maps equally well to two positions on the genome (multi-mapped read), its mapQ score will be set to 2. The read in the pair with the higher mapQ is used for the pair.
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316 - Pairs must be above some minimum nucleotide identity (ANI) value. For example if reads in a pair are 100bp each, and each read has a single mismatch, the ANI of that pair would be 0.99
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317
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318 Next, using only read pairs that pass filters, a number of microdiversity metrics are calculated on a scaffold-by-scaffold basis. This includes:
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319
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320 - Calculate the coverage at each position along the scaffold
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321 - Calculate the nucleotide diversity at each position along the scaffold in which the coverage is greater than the min_cov argument.
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322 - Identify SNSs and SNVs. The criteria for being reported as a divergent site are 1) More than min_cov number of bases at that position, 2) More than min_freq percentage of reads that are a variant base, 3) The number of reads with the variant base is more than the null model for that coverage.
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323 - Calculate linkage between divergent sites on the same read pair. For each pair harboring a divergent site, calculate the linkage of that site with other divergent sites within that same pair. This is only done for pairs of divergent sites that are both on at least MIN_SNP reads
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324 - Calculate scaffold-level properties. These include things like the overall coverage, breadth of coverage, average nucleotide identity (ANI) between the reads and the reference genome, and the expected breadth of coverage based on that true coverage.
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325
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326 Finally, this information is stored as an IS_profile object. This includes the locations of divergent sites, the number of read pairs that passed filters (and other information) for each scaffold, the linkage between SNV pairs, ect.
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327
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328 Inputs
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329 ======
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330
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331 A fasta file and a bam/sam file,
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332
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333 Output
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334 ======
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335
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336 An IS_profile. (Zip file), Containing:
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337
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338 1. scaffold_info.tsv
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339
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340 This gives basic information about the scaffolds in your sample at the highest allowed level of read identity.
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341
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342 2. mapping_info.tsv
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343
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344 This provides an overview of the number of reads that map to each scaffold, and some basic metrics about their quality.
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345
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346 3. SNVs.tsv
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347
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348 This describes the SNVs and SNSs that are detected in this mapping. While we should refer to these mutations as divergent sites, sometimes SNV is used to refer to both SNVs and SNSs.
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349
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350 4. linkage.tsv
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351
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352 This describes the linkage between pairs of SNPs in the mapping that are found on the same read pair at least min_snp times.
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353
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354 5. gene_info.tsv
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355
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356 This describes some basic information about the genes being profiled.
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357
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358 6. genome_info.tsv
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359
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360 Describes many of the above metrics on a genome-by-genome level, rather than a scaffold-by-scaffold level. (To output it, set --skip_genome_wide to false)
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361
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362 7. Figures/Plots (When --skip_plot_generation is set to false):
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363
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364 - Coverage and breadth vs. read mismatches
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365 - Genome-wide microdiversity metrics
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366 - Read-level ANI distribution
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367 - Major allele frequencies
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368 - Linkage decay
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369 - Read filtering plots
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370 - Scaffold inspection plot (large)
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371 - Linkage with SNP type (GENES REQUIRED)
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372 - Gene histograms (GENES REQUIRED)
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373
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374 ]]></help>
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375 <citations>
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376 <citation type="doi">10.1101/2020.01.22.915579</citation>
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377 </citations>
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378 </tool>