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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain commit aa7c7a35834f36dad6e72d5f54089a578be60731
author iuc
date Thu, 02 Nov 2023 14:59:48 +0000
parents dff92aac9f75
children
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1 <tool id="instrain_compare" name="InStrain Compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Compares multiple inStrain profiles (popANI, coverage_overlap, etc.) </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
3
92a7945118a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain commit aa7c7a35834f36dad6e72d5f54089a578be60731
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6 <expand macro="biotools"/>
0
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7 <expand macro="requirements"/>
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8 <version_command>inStrain compare --version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $stb
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11 ln -s '$stb' 'stb_file.stb' &&
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12 #end if
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13 #if $other.genome
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14 ln -s '$other.genome' 'genome_file.stb' &&
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15 #end if
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16 #for $i, $s in enumerate($input_is)
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17 #if $s
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18 input_count=$i
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19 mkdir -p $i-input.IS &&
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20 unzip '$s' -d '$i-input.IS/' &&
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21 #end if
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22 #end for
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23 inStrain compare
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24 --input
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25 #for $i, $s in enumerate($input_is)
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26 #if $s
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27 '$i-input.IS'
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28 #end if
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29 #end for
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30 --output 'output.IS.COMPARE'
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31 --processes "\${GALAXY_SLOTS:-6}"
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32 #if $stb
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33 --stb 'stb_file.stb'
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34 #end if
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35 --min_cov $variant_calling.min_cov
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36 --min_freq $variant_calling.min_freq
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37 --fdr $variant_calling.fdr
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38 $database.database_mode
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39 --breadth $database.breadth
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40 #if $other.scaffolds
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41 --scaffolds '$other.scaffolds'
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42 #end if
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43 #if $other.genome
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44 --genome 'genome_file.stb'
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45 #end if
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46 $other.store_coverage_overlap
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47 $other.store_mismatch_locations
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48 $other.include_self_comparisons
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49 $other.skip_plot_generation
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50 --group_length $other.group_length
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51 --ani_threshold $genome_clustering.ani_threshold
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52 --coverage_treshold $genome_clustering.coverage_treshold
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53 --clusterAlg '$genome_clustering.clusterAlg'
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54 ]]></command>
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55 <inputs>
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56 <param name="input_is" type="data" format="zip" multiple="true" label="inStrain Profile IS folder" help=" The Zip files for the IS profiles outputs you want to compare"/>
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57 <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"/>
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58 <section name="variant_calling" title="Variant Calling Options" expanded="true">
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59 <param argument="--min_cov" type="integer" value="5" label=" Minimum coverage to call an variant"/>
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60 <param argument="--min_freq" type="float" value="0.05" label="Minimum SNP frequency to confirm a SNV" help="Both this AND the FDR snp count cutoff must be true to call a SNP."/>
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61 <param argument="--fdr" type="float" value="1e-06" min="0" max="1" help="SNP false discovery rate- based on simulation data with a 0.1 percent error rate (Q30)"/>
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62 </section>
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63 <section name="database" title="Database Mode Parameters" expanded="true">
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64 <param argument="--database_mode" type="boolean" truevalue="--debugdatabase_mode" falsevalue="" checked="false" label="Automatically determine which genomes are present in each Profile and only compare scaffolds from those genomes." help="All profiles must have run Profile with the same .stb"/>
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65 <param argument="--breadth" type="float" value="0.5" label="Minimum breadth_minCov required to count a genome present"/>
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66 </section>
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67 <section name="other" title="Other Options" expanded="true">
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68 <param argument="--scaffolds" type="data" format="fasta" optional="true" label="Location to a list of scaffolds to compare. You can also make this a .fasta file and it will load the scaffold names"/>
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69 <param argument="--genome" type="data" format="tabular" optional="true" label="Run scaffolds belonging to this single genome only. Must provide an .stb file"/>
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70 <param argument="--store_coverage_overlap" type="boolean" truevalue="--store_coverage_overlap" falsevalue="" checked="false" label="Store coverage overlap on an mm level"/>
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71 <param argument="--store_mismatch_locations" type="boolean" truevalue="--store_mismatch_locations" falsevalue="" checked="false" label="Store the locations of SNPs"/>
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72 <param argument="--include_self_comparisons" type="boolean" truevalue="--include_self_comparisons" falsevalue="" checked="false" label="Compare IS profiles against themself"/>
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73 <param argument="--skip_plot_generation" type="boolean" truevalue="--skip_plot_generation" falsevalue="" checked="false" label="Dont create plots at the end of the run"/>
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74 <param argument="--group_length" type="integer" value="10000000" label="How many bp to compare simultaneously" help="higher will use more RAM and run more quickly"/>
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75 </section>
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76 <section name="genome_clustering" title="Genome Clustering Options" expanded="true">
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77 <param argument="--ani_threshold" type="float" value="0.99999" label="popANI threshold to cluster genomes at" help="Must provide .stb file to do so"/>
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78 <param argument="--coverage_treshold" type="float" value="0.1" label="Minimum percent_genome_compared for a genome comparison to count" help="if below the popANI will be set to 0"/>
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79 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes">
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80 <option value="average" selected="true">Average</option>
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81 <option value="single">Single</option>
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82 <option value="ward">Ward</option>
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83 <option value="complete">complete</option>
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84 <option value="centroid">centroid</option>
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85 <option value="weighted">weighted</option>
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86 <option value="median">median</option>
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87 </param>
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88 </section>
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89 </inputs>
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90 <outputs>
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91 <data name="comparisonsTable" format="tabular" from_work_dir="output.IS.COMPARE/output/output.IS.COMPARE_comparisonsTable.tsv" label="Comparisons Table: Summarizes the differences between two inStrain profiles on a scaffold by scaffold level" />
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
92 <data name="pairwise_SNP_locations" format="tabular" from_work_dir="output.IS.COMPARE/output/output.IS.COMPARE_pairwise_SNP_locations.tsv" label="Pairwise SNP locations: Lists the locations of all differences between profiles." />
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
93 <data name="genomeWide_compare" format="tabular" from_work_dir="output.IS.COMPARE/output/output.IS.COMPARE_genomeWide_compare.tsv" label="Genome Wide compare: A genome-level summary of the differences detected by inStrain compare." />
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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94 <data format="tabular" name="strain_clusters" from_work_dir="output.IS.COMPARE/output/output.IS.COMPARE_strain_clusters.tsv" label="Strain clusters: Generate strain-level clusters" />
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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95 <data format="pdf" name="inStrainCompare_dendrograms" from_work_dir="output.IS.COMPARE/figures/output.IS.COMPARE_inStrainCompare_dendrograms.pdf" label="inStrain Compare dendrograms: genomeWide microdiveristy metrics" />
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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96 </outputs>
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97 <tests>
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98 <test expect_num_outputs="5">
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99 <param name="stb" value="N5_271_010G1.maxbin2.stb"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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100 <param name="input_is" value="N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.IS.zip,N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.IS.zip"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
101 <section name="variant_calling">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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102 <param name="min_cov" value="5"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
103 <param name="min_freq" value="0.05"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
104 <param name="fdr" value="1e-06"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
105 </section>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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106 <section name="database">
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diff changeset
107 <param name="database_mode" value="false"/>
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108 <param name="breadth" value="0.5"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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109 </section>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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110 <section name="other">
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111 <param name="store_coverage_overlap" value="false"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
112 <param name="store_mismatch_locations" value="false"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
113 <param name="include_self_comparisons" value="false"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
114 <param name="skip_plot_generation" value="false"/>
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diff changeset
115 <param name="group_length" value="10000000"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
116 </section>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
117 <section name="genome_clustering">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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118 <param name="ani_threshold" value="0.99999"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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119 <param name="coverage_treshold" value="0.1"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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120 <param name="clusterAlg" value="average"/>
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121 </section>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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122 <output name="comparisonsTable">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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123 <assert_contents>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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124 <has_text text="N5_271_010G1_scaffold_73"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
125 <has_n_lines n="168"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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126 <has_n_columns n="11"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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127 </assert_contents>
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128 </output>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
129 <output name="pairwise_SNP_locations">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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130 <assert_contents>
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131 <has_n_lines n="0"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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132 </assert_contents>
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133 </output>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
134 <output name="genomeWide_compare">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
135 <assert_contents>
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diff changeset
136 <has_text text="name1"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
137 <has_n_lines n="3"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
138 <has_n_columns n="10"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
139 </assert_contents>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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140 </output>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
141 <output name="strain_clusters">
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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142 <assert_contents>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
143 <has_text text="1_1"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
144 <has_n_lines n="5"/>
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diff changeset
145 <has_n_columns n="3"/>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
146 </assert_contents>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
147 </output>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
148 <output name="inStrainCompare_dendrograms">
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diff changeset
149 <assert_contents>
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150 <has_size value="384512" delta="10000" />
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diff changeset
151 </assert_contents>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
152 </output>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
153 </test>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
154 </tests>
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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155 <help><![CDATA[
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diff changeset
156 @HELP_HEADER@
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157
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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158 Compare
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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parents:
diff changeset
159 =======
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
160
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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parents:
diff changeset
161 is part of the inStrain module that provides the ability to compare multiple inStrain profiles (created by running inStrain profile).
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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162
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
163 Note
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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parents:
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164 ====
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
165
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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166 inStrain can only compare inStrain profiles that have been mapped to the same .fasta file
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diff changeset
167
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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168 inStrain compare does pairwise comparisons between each input inStrain profile. For each pair, a series of steps are undertaken:
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
169
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170 1. All positions in which both IS_profile objects have at least min_cov coverage (5x by default) are identified. This information can be stored in the output by using the flag –store_coverage_overlap, but due to it’s size, it’s not stored by default.
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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171
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172
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
173 2. Each position identified in step 1 is compared to calculate both conANI and popANI. The way that it compares positions is by testing whether the consensus base in sample 1 is detected at all in sample 2 and vice-versa. Detection of an allele in a sample is based on that allele being above the set -min_freq and -fdr. All detected differences between each pair of samples can be reported if the flag –store_mismatch_locations is set.
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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174
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
175
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
176 3. The coverage overlap and the average nucleotide identity for each scaffold is reported. For details on how this is done.
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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177
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178
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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179 Inputs
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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180 ======
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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181
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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182 Multiple inStrain profiles IS outputs (zip files), all mapped to the same .fasta file
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183
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184
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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185 Outputs
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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186 =======
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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187
dff92aac9f75 "planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
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diff changeset
188 1. comparisonsTable.tsv
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189
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190 Summarizes the differences between two inStrain profiles on a scaffold by scaffold level
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191
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192 2. pairwise_SNP_locations.tsv
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193
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194 Lists the locations of all differences between profiles. Because it’s a big file, this will only be created is you include the flag --store_mismatch_locations in your inStrain compare command.
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195
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196 3. genomeWide_compare.tsv
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197
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198 A genome-level summary of the differences detected by inStrain compare. Generated by running inStrain genome_wide on the results of inStrain compare
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199
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200 4. strain_clusters.tsv
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201
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202 The result of clustering the pairwise comparison data provided in genomeWide_compare.tsv to generate strain-level clusters. Performed using hierarchical clustering in the same manner as the program dRep
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203
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204 5. Compare dendrograms (PDF) figure/plot
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205
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206 A dendrogram comparing all samples based on popANI and based on shared_bases.
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207
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208 ]]></help>
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209 <citations>
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210 <citation type="doi">10.1101/2020.01.22.915579</citation>
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211 </citations>
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212 </tool>