Mercurial > repos > iuc > instrain_compare
changeset 0:dff92aac9f75 draft
"planemo upload for repository https://github.com/MrOlm/inStrain commit e6eae71231e551c08aa96afc9f15b8ba87676101"
| author | iuc |
|---|---|
| date | Wed, 11 Aug 2021 21:11:53 +0000 |
| parents | |
| children | 3b54b419b5cb |
| files | instrain_compare.xml macros.xml test-data/N5_271_010G1.maxbin2.stb test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G1.IS.zip test-data/N5_271_010G1_scaffold_min1000.fa-vs-N5_271_010G2.IS.zip test-data/SmallScaffold.fa test-data/SmallScaffold.fa.sorted.bam |
| diffstat | 7 files changed, 421 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/instrain_compare.xml Wed Aug 11 21:11:53 2021 +0000 @@ -0,0 +1,212 @@ +<tool id="instrain_compare" name="InStrain Compare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Compares multiple inStrain profiles (popANI, coverage_overlap, etc.) </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="edam_ontology"/> + <expand macro="requirements"/> + <version_command>inStrain compare --version</version_command> + <command detect_errors="exit_code"><![CDATA[ +#if $stb + ln -s '$stb' 'stb_file.stb' && +#end if +#if $other.genome + ln -s '$other.genome' 'genome_file.stb' && +#end if +#for $i, $s in enumerate($input_is) + #if $s + input_count=$i + mkdir -p $i-input.IS && + unzip '$s' -d '$i-input.IS/' && + #end if +#end for +inStrain compare + --input + #for $i, $s in enumerate($input_is) + #if $s + '$i-input.IS' + #end if + #end for + --output 'output.IS.COMPARE' + --processes "\${GALAXY_SLOTS:-6}" +#if $stb + --stb 'stb_file.stb' +#end if + --min_cov $variant_calling.min_cov + --min_freq $variant_calling.min_freq + --fdr $variant_calling.fdr + $database.database_mode + --breadth $database.breadth +#if $other.scaffolds + --scaffolds '$other.scaffolds' +#end if +#if $other.genome + --genome 'genome_file.stb' +#end if + $other.store_coverage_overlap + $other.store_mismatch_locations + $other.include_self_comparisons + $other.skip_plot_generation + --group_length $other.group_length + --ani_threshold $genome_clustering.ani_threshold + --coverage_treshold $genome_clustering.coverage_treshold + --clusterAlg '$genome_clustering.clusterAlg' + ]]></command> + <inputs> + <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"/> + <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"/> + <section name="variant_calling" title="Variant Calling Options" expanded="true"> + <param argument="--min_cov" type="integer" value="5" label=" Minimum coverage to call an variant"/> + <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."/> + <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)"/> + </section> + <section name="database" title="Database Mode Parameters" expanded="true"> + <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"/> + <param argument="--breadth" type="float" value="0.5" label="Minimum breadth_minCov required to count a genome present"/> + </section> + <section name="other" title="Other Options" expanded="true"> + <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"/> + <param argument="--genome" type="data" format="tabular" optional="true" label="Run scaffolds belonging to this single genome only. Must provide an .stb file"/> + <param argument="--store_coverage_overlap" type="boolean" truevalue="--store_coverage_overlap" falsevalue="" checked="false" label="Store coverage overlap on an mm level"/> + <param argument="--store_mismatch_locations" type="boolean" truevalue="--store_mismatch_locations" falsevalue="" checked="false" label="Store the locations of SNPs"/> + <param argument="--include_self_comparisons" type="boolean" truevalue="--include_self_comparisons" falsevalue="" checked="false" label="Compare IS profiles against themself"/> + <param argument="--skip_plot_generation" type="boolean" truevalue="--skip_plot_generation" falsevalue="" checked="false" label="Dont create plots at the end of the run"/> + <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"/> + </section> + <section name="genome_clustering" title="Genome Clustering Options" expanded="true"> + <param argument="--ani_threshold" type="float" value="0.99999" label="popANI threshold to cluster genomes at" help="Must provide .stb file to do so"/> + <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"/> + <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes"> + <option value="average" selected="true">Average</option> + <option value="single">Single</option> + <option value="ward">Ward</option> + <option value="complete">complete</option> + <option value="centroid">centroid</option> + <option value="weighted">weighted</option> + <option value="median">median</option> + </param> + </section> + </inputs> + <outputs> + <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" /> + <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." /> + <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." /> + <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" /> + <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" /> + </outputs> + <tests> + <test expect_num_outputs="5"> + <param name="stb" value="N5_271_010G1.maxbin2.stb"/> + <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"/> + <section name="variant_calling"> + <param name="min_cov" value="5"/> + <param name="min_freq" value="0.05"/> + <param name="fdr" value="1e-06"/> + </section> + <section name="database"> + <param name="database_mode" value="false"/> + <param name="breadth" value="0.5"/> + </section> + <section name="other"> + <param name="store_coverage_overlap" value="false"/> + <param name="store_mismatch_locations" value="false"/> + <param name="include_self_comparisons" value="false"/> + <param name="skip_plot_generation" value="false"/> + <param name="group_length" value="10000000"/> + </section> + <section name="genome_clustering"> + <param name="ani_threshold" value="0.99999"/> + <param name="coverage_treshold" value="0.1"/> + <param name="clusterAlg" value="average"/> + </section> + <output name="comparisonsTable"> + <assert_contents> + <has_text text="N5_271_010G1_scaffold_73"/> + <has_n_lines n="168"/> + <has_n_columns n="11"/> + </assert_contents> + </output> + <output name="pairwise_SNP_locations"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="genomeWide_compare"> + <assert_contents> + <has_text text="name1"/> + <has_n_lines n="3"/> + <has_n_columns n="10"/> + </assert_contents> + </output> + <output name="strain_clusters"> + <assert_contents> + <has_text text="1_1"/> + <has_n_lines n="5"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output name="inStrainCompare_dendrograms"> + <assert_contents> + <has_size value="384512" delta="10000" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +Compare +======= + +is part of the inStrain module that provides the ability to compare multiple inStrain profiles (created by running inStrain profile). + +Note +==== + +inStrain can only compare inStrain profiles that have been mapped to the same .fasta file + +inStrain compare does pairwise comparisons between each input inStrain profile. For each pair, a series of steps are undertaken: + +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. + + +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. + + +3. The coverage overlap and the average nucleotide identity for each scaffold is reported. For details on how this is done. + + +Inputs +====== + +Multiple inStrain profiles IS outputs (zip files), all mapped to the same .fasta file + + +Outputs +======= + +1. comparisonsTable.tsv + + Summarizes the differences between two inStrain profiles on a scaffold by scaffold level + +2. pairwise_SNP_locations.tsv + + 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. + +3. genomeWide_compare.tsv + + A genome-level summary of the differences detected by inStrain compare. Generated by running inStrain genome_wide on the results of inStrain compare + +4. strain_clusters.tsv + + 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 + +5. Compare dendrograms (PDF) figure/plot + + A dendrogram comparing all samples based on popANI and based on shared_bases. + + ]]></help> + <citations> + <citation type="doi">10.1101/2020.01.22.915579</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Aug 11 21:11:53 2021 +0000 @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.5.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">20.01</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0796</edam_topic> + <edam_topic>topic_3174</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0484</edam_operation> + <edam_operation>operation_3209</edam_operation> + <edam_operation>operation_3730</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">instrain</requirement> + <yield/> + </requirements> + </xml> + <token name="@HELP_HEADER@"> +What it does +============ + +inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification. + +Read more about the tool: https://instrain.readthedocs.io/en/latest/ + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/2020.01.22.915579</citation> + </citations> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/N5_271_010G1.maxbin2.stb Wed Aug 11 21:11:53 2021 +0000 @@ -0,0 +1,167 @@ +N5_271_010G1_scaffold_0 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_1 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_2 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_3 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_4 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_5 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_6 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_7 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_8 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_9 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_10 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_11 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_12 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_13 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_14 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_15 maxbin2.maxbin.001.fasta +N5_271_010G1_scaffold_16 maxbin2.maxbin.001.fasta 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SmallScaffold.fa Wed Aug 11 21:11:53 2021 +0000 @@ -0,0 +1,6 @@ +>WeirdBoi +AAAAAAAAAAAAAAAAAAAAAAA +>N5_271_010G1_scaffold_963 read_length_150 read_count_3782 +TCTCCATTACATTCCATTCCATTCGGGTTGTTCCATTCCATTCCATTCCA +TTCCACTCCATTCCATTGCACTCGGGTTGATTCCATTCCATTCCATTCCG +GATGATTCCATTCCATTGCATTCCGT