| Previous changeset 0:134e4e78e754 (2022-04-26) Next changeset 2:5bf5792b0996 (2023-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112 |
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modified:
coverm_genome.xml macros.xml test-data/test5.tsv |
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added:
test-data/test4_cluster.tsv test-data/test4_rep.fa test-data/test4_rep1.fa test-data/test4_rep2.fa test-data/test4_rep3.fa |
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| diff -r 134e4e78e754 -r a671907f96fe coverm_genome.xml --- a/coverm_genome.xml Tue Apr 26 15:27:01 2022 +0000 +++ b/coverm_genome.xml Tue Jan 24 12:32:54 2023 +0000 |
| [ |
| @@ -1,5 +1,5 @@ -<tool id="coverm_genome" name="CoverM-GENOME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> - <description>read coverage and relative abundance calculator focused on metagenomics applications</description> +<tool id="coverm_genome" name="CoverM genome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Calculate coverage of individual genomes</description> <macros> <import>macros.xml</import> </macros> @@ -135,7 +135,7 @@ ln -s '$input_file' '$file_path' && $ref_files.append($file_path) #end for - #if $reads.genome.add_genome.add_genome + #if $reads.genome.add_genome.add_genome == "true" mkdir -p genomes && #set genome_files = [] #if $reads.genome.add_genome.add_genomic == "history" @@ -156,7 +156,8 @@ #end if #end if #end if - + + mkdir ./representative-fasta/ && coverm genome #if $reads.read_type == 'paired' -1 @@ -240,7 +241,7 @@ -s "$reads.genome.cond_single_genome.separator" #end if #end if - #if $reads.genome.add_genome.add_genome + #if $reads.genome.add_genome.add_genome == "true" -f #for $genome in $genome_files '${genome}' @@ -255,27 +256,27 @@ $derep.dereplicate #if $derep.checkm_tab_table: - --chekm-tab-table $derep.checkm_tab_table + --chekm-tab-table '$derep.checkm_tab_table' #end if #if $derep.genome_info: - --genome-info $derep.genome_info + --genome-info '$derep.genome_info' #end if - #if $derep.min_completeness: + #if $derep.min_completeness != "": --min-completeness $derep.min_completeness #end if - #if $derep.max_contamination: + #if $derep.max_contamination != "": --max-contamination $derep.max_contamination #end if - #if $derep.dereplication_ani: + #if $derep.dereplication_ani != "": --dereplication-ani $derep.dereplication_ani #end if - #if $derep.dereplication_aligned_fraction: + #if $derep.dereplication_aligned_fraction != "": --dereplication-aligned-fraction $derep.dereplication_aligned_fraction #end if - #if $derep.dereplication_fragment_length: + #if $derep.dereplication_fragment_length != "": --dereplication-fragment-length $derep.dereplication_fragment_length #end if - #if $derep.dereplication_prethreshold_ani: + #if $derep.dereplication_prethreshold_ani != "": --dereplication-prethreshold-ani $derep.dereplication_prethreshold_ani #end if #if $derep.dereplication_quality_formula: @@ -315,13 +316,13 @@ --methods $cov.relative_abundance $cov.mean $cov.cond_methods.trimmed_mean $cov.covered_bases $cov.covered_fraction $cov.variance $cov.length $cov.count $cov.metabat $cov.coverage_histogram $cov.reads_per_base $cov.rpkm $cov.tpm - #if $cov.min_covered_fraction: + #if $cov.min_covered_fraction != "": --min-covered-fraction $cov.min_covered_fraction #end if - #if $cov.contig_end_exclusion: + #if $cov.contig_end_exclusion != "": --contig-end-exclusion $cov.contig_end_exclusion #end if - #if $cov.cond_methods.trimmed_mean + #if $cov.cond_methods.trimmed_mean == "trimmed_mean" #if $cov.cond_methods.trim_min: --trim-min $cov.cond_methods.trim_min #end if @@ -334,15 +335,18 @@ --output-format $out.output_format #end if #if $out.dereplication_output_cluster_definition: - --dereplication-output-cluster-definition + --dereplication-output-cluster-definition '$cluster_definition' #end if #if $out.dereplication_output_representative_fasta_directory_copy: - --dereplication-output-representative-fasta-directory-copy . + --dereplication-output-representative-fasta-directory-copy ./representative-fasta/ #end if $out.no_zeros --output-file output.tsv --threads \${GALAXY_SLOTS:-1} - 2> stdout.txt + + #if $derep.dereplicate and $out.dereplication_output_cluster_definition + && sed -i -e 's@genomes/@@g; s/\.fna//g' '$cluster_definition' + #end if ]]></command> <inputs> <expand macro="reads" /> @@ -394,12 +398,16 @@ </inputs> <outputs> <data name="output1" format="tsv" from_work_dir="./output.tsv"/> - <data name="cluster-definition" format="tsv"> - <filter>out['dereplication_output_cluster_definition']</filter> + <data name="cluster_definition" format="tsv" label="${tool.name} on ${on_string}: cluster definition"> + <filter>derep['dereplicate'] and out['dereplication_output_cluster_definition']</filter> </data> + <collection name="representative_fasta" type="list" label="${tool.name} on ${on_string}: representative fasta"> + <discover_datasets pattern="(?P<designation>.*)\.fna" format="fasta" directory="representative-fasta" /> + <filter>derep['dereplicate'] and out['dereplication_output_representative_fasta_directory_copy']</filter> + </collection> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <conditional name="reads"> <param name="read_type" value="paired_collection"/> <param name="paired_reads"> @@ -489,7 +497,7 @@ </assert_contents> </output> </test> - <test expect_num_outputs="1"> + <test expect_num_outputs="3"> <conditional name="reads"> <param name="read_type" value="paired_collection"/> <param name="paired_reads"> @@ -513,7 +521,20 @@ <section name="cov"> <param name="mean" value="true"/> </section> + <section name="derep"> + <param name="dereplicate" value="true"/> + </section> + <section name="out"> + <param name="dereplication_output_cluster_definition" value="true"/> + <param name="dereplication_output_representative_fasta_directory_copy" value="true"/> + </section> <output name="output1" file="test3.tsv" ftype="tsv"/> + <output name="cluster_definition" ftype="tsv" value="test4_cluster.tsv"/> + <output_collection name="representative_fasta" type="list" count="3"> + <element name="genome1" file="test4_rep1.fa" ftype="fasta" /> + <element name="genome2" file="test4_rep2.fa" ftype="fasta" /> + <element name="genome3" file="test4_rep3.fa" ftype="fasta" /> + </output_collection> </test> <test expect_num_outputs="1"> <conditional name="reads"> |
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| diff -r 134e4e78e754 -r a671907f96fe macros.xml --- a/macros.xml Tue Apr 26 15:27:01 2022 +0000 +++ b/macros.xml Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -1,12 +1,13 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package">coverm</requirement> + <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> </requirements> </xml> <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> - <token name="@TOOL_VERSION@">0.2.1</token> + <token name="@TOOL_VERSION@">0.6.1</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> <xml name="citation"> <citations> <citation type="bibtex"> @@ -96,7 +97,10 @@ </when> </conditional> <conditional name="add_genome"> - <param name="add_genome" type="boolean" label="Add additional Genome Files"/> + <param name="add_genome" type="select" label="Add additional Genome Files"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> <when value="true"> <conditional name="add_genomic"> <param type="select" label="Reference genome source" name="source"> @@ -186,7 +190,7 @@ <xml name="add_reads"> <section name="add_reads" title="Add an additional read"> <conditional name="extra_read"> - <param type="select" label="Read type" optional="true" name="read_type"> + <param type="select" label="Read type" name="read_type"> <option value="none" selected="true">None</option> <option value="paired">Paired end</option> <option value="paired_collection">Paired collection</option> @@ -251,7 +255,10 @@ <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/> <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/> <conditional name="cond_methods"> - <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/> + <param name="trimmed_mean" type="select" label="Trimmed mean"> + <option value="trimmed_mean">Yes</option> + <option value="" selected="true">No</option> + </param> <when value="trimmed_mean"> <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/> <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/> |
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| diff -r 134e4e78e754 -r a671907f96fe test-data/test4_cluster.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_cluster.tsv Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -0,0 +1,3 @@ +genome1 genome1 +genome2 genome2 +genome3 genome3 |
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| diff -r 134e4e78e754 -r a671907f96fe test-data/test4_rep1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep1.fa Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +GAACATGGGGGGTTGTACACCGCTGGCAGGATATAAAAGAGCGAATTCTTCGTGGTGGGATGCAGAATGTTCATGCACCGCAAACCTTAGGCCCTACCCAATAACAGTCAGCTCCTCCCCTAGAAATACCGTGTCTACGTGTATGTAATGTCAAAACCGCGCTGGTCCATAACTGACCACGACATACGCTTAAGCGACGCAGGTCCCCGTTTATGGACGCAGTAAGATGATATGACAGTAACAGAACGAACGCCTTGATAGCCACTTGGCCTGGTGCCAACGGGGAACGACCTATAGGGGCCAAATTGATTCCAGCTGGTCGGGTGCGCGTATCATCCAATCCAGCCAGGCAGCAACCTCGTATAAGCATCCACACAGCGAGATTTCCAGGACCTTTGAGACGCATCTAGCAGTTTTCCCCCCTTCCACTGACACGTAGTTGATCAAATATCTCGTGTCCACCGGAATCCTCAGAGATTCTCTTCTGTCAAAAAACACTC +>random_sequence_length_500_2 +CGCTCATGTGCCAAGCATGGACGCCGGAGACACATTTGCTAGTCGGGATGTACGCGGTCTTGTCCACTCTAAAGGGTAAATACAGGAAGCGGTCTCTAGGGACGGGCACTTAATGTAGTTGCATTTATCGATCGCGGGTCCAGATCTGATAGCCGTGCTATGCACATACGATGCTCATAACGCGCGTGATTCCCTTCATTAAGGTACGGCTACCCTGCACCTCTAGACTTGTTTGTACTATCTAGAGCAGTGAGTCGAGCGTCGACAATAGGGTCAGGGCCGGGTACTATTTTGAGCTTTACGGTAATTGCCTTGGGCTAGTAAAACCGCTTCTATACCGCAGACTCATCGAATAATGATTCCTGCAAAACGAGCACGATACGGGAGTTCCTTATGACCAGTCTAATGGTCTCAAGGGTCTCCCCCGGGGAATTACGGTGCCAAGAATGTCTCTGTAATTGACCTAAGTTGTCTGTCGATCCAGAAAATCTGACCAAGAT |
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| diff -r 134e4e78e754 -r a671907f96fe test-data/test4_rep2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep2.fa Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +TCATGAACGGTAGTCAGTCAAGTTTCGCCAGCAATAGGCACAGCTTGTATGGAGGGGTTTAGTCGCCGGAGTGTTACGAGTTTGACGATCCAAAGTTGGAGTCGCCGTGATAATTAATGATATTGCGTCTTCGGTGGGCACGATGAGCCAATCTGCGTCGCACTAGTTTACGTGTTAACGTAGTGAACCTAGACATGACGGGACTATGGCAGTAAGCCGTCACAGCATGTCGGTTCCGGACCACGAGGGTCCATAAGACTAACGATCCACGCTAATTGGCGGATTTACCAAGGCGTCTTCTCTGCGTGTAAGACCCACACCGTGCCTCTGTACCTATGGACGTGCGCGACCATCTTATGATATGAGCATCACATGTTTAATAGAGCGTCCGGTGTCCCTGTAATGCCACCACTTCTGTTTCAACGGACGCTGAATCTAAGCCGATATTTTTGCCTTGATCAGAACGGGGCAGTGAAGGAGCTGCACTAAACTGGCCCTTA +>random_sequence_length_500_2 +GGATCGGATTACTAATGTTTTTCCAGTCGCCTGTTACTCCAGGCGCGGATGCGAGTGGTCTTTGCCAAGTAGCCCCATGCCACCTGTACAAGGCGGACAAACGCGGATGCGTTTGCATAAATTACCACCGTAAGATACGTTGGCGTATTGCCGTACAAAGGCGGACAGTCCAGATATTTCTTCGGATGTAATTATTGTAGGCGTGCACAACCTACTAGGCGAAAGAGCGGCCCGTTAATCGCGGGTCGCGCCGTGCCCAATTGAACACTTTGCCACGCACGTGACTGGCGGACGGCTCACACGCTATCTCCAAAAATCTACACTTCCGGAGCTAGGCTCCATGACAGGGATGTTCTTATTCAACAAGATGGAGTGCTAATATTAACAATCGACGACACAGGTGAAAAACCTCTTGTCATGTAGCTAGCAGTTATGCGGGCGTACACACTAGTGCTAATCTACTAATCATCCACGGGCCCCTGCTAGAGATCCAAAGGGGT |
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| diff -r 134e4e78e754 -r a671907f96fe test-data/test4_rep3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep3.fa Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -0,0 +1,4 @@ +>random_sequence_length_500_1 +AGAGGGAGCCTTGCGTCGGTGCTCCACGTCGTAAAGCCGTTGAGACCGCGATTACTTTGTTTATTTTCAATTCACTTGTCACAATCAGAAGGACACCGGCGACGGCCAGTTTCCATCGCCCGTCCAGGGTATCGGGGTACCTCTCTACTCGAACGTCTGCGGGGGTTTATCGGGTCTTTACAGGGGGACCAAATGGTTGGACACGGTACCTCAACGCGATAATATATGTCCTGAGTGTGATCATCGGCTGCTTGATTGACTAGTAAGTAAATAACTCCGCCCGCCGAAAGTGACCATTCTAGGAAAATACCCTCTAGCCTCTTGCTTTTGTACGGACTCACTTTCAACGTCCAGGGGTTGCGAACTAATACAGTGAAAGCGATGACCGACAGTAGCAGTTGAGTCTCCCAATGCACCGGTCCCTAACCTCAACCCGGCGTCTAGTCTGACCAGCCTATACAGATAGCAAACAACGTGGACGCGACGGACATGACGAAATA +>random_sequence_length_500_2 +GCTACTTTACCGTGCGGAAGTAGGTGGGTAGGCCCACATCCTCGTCCTTCAGTGGGCACCCATCTCTCTAAGTACATCTCAAGTGAGGAGGGCTGAGAAAATTGGACGATCTAGTGGAAGCGCGCCGAAATATGGCCTGAGTGAGATCGACCCCGAGGAGCGAGCTCGTTTTCCGAAGTTCGTTATGAGTATGGCGTTCGTTGCTGGCCGAGTACCCCCTGGTGACGTAAAGTGTTTATTTACACAGCTACTTCTCCGAACCAACGACTTATATGTGGGTCCCTGATTGCCTCCCATAGGTCCGGCATAGTTAAGAAAGTTAACGGAACCAAAGTCCAGTACATGGAGTTCTATGATAGACAGCTGTCTCCATTCCCGTATCTGCCAAAGAGATTAGATCCTAGTTGATCCCAGCAGCTACTCGTAATGACAGGATCCGGCGTGTCACTATACGACGCTTGCGGGAGGATGGTCGCCCTGCCCGTACCGTTACTTAGATC |
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| diff -r 134e4e78e754 -r a671907f96fe test-data/test5.tsv --- a/test-data/test5.tsv Tue Apr 26 15:27:01 2022 +0000 +++ b/test-data/test5.tsv Tue Jan 24 12:32:54 2023 +0000 |
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| @@ -0,0 +1,2 @@ +Genome 2seqs.bad_read.1.with_supplementary Read Count +genome1 20 |