Mercurial > repos > iuc > instrain_compare
view instrain_compare.xml @ 1:3b54b419b5cb draft
"planemo upload for repository https://github.com/MrOlm/inStrain commit 0b4dfba748b795669e01561d6ebf5f551201e503"
author | iuc |
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date | Tue, 09 Nov 2021 15:15:08 +0000 |
parents | dff92aac9f75 |
children | 92a7945118a9 |
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<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>