| Previous changeset 0:6941d0d453ba (2022-04-26) Next changeset 2:f8cb3f0a19fa (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_contig.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 6941d0d453ba -r 688a777e1b19 coverm_contig.xml --- a/coverm_contig.xml Tue Apr 26 15:27:37 2022 +0000 +++ b/coverm_contig.xml Tue Jan 24 12:33:11 2023 +0000 |
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| @@ -1,8 +1,7 @@ -<tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5"> +<tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Calculate coverage of individual contigs</description> <macros> <import>macros.xml</import> - <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token> - <token name="@TOOL_VERSION@">0.2.1</token> </macros> <expand macro="requirements"/> <command><![CDATA[ @@ -224,7 +223,7 @@ #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 @@ -238,7 +237,6 @@ #end if --output-file output.tsv --threads \${GALAXY_SLOTS:-1} - 2> stdout.txt ]]></command> <inputs> <expand macro="reads_for_contig" /> |
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| diff -r 6941d0d453ba -r 688a777e1b19 macros.xml --- a/macros.xml Tue Apr 26 15:27:37 2022 +0000 +++ b/macros.xml Tue Jan 24 12:33:11 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 6941d0d453ba -r 688a777e1b19 test-data/test4_cluster.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_cluster.tsv Tue Jan 24 12:33:11 2023 +0000 |
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| @@ -0,0 +1,3 @@ +genome1 genome1 +genome2 genome2 +genome3 genome3 |
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| diff -r 6941d0d453ba -r 688a777e1b19 test-data/test4_rep1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep1.fa Tue Jan 24 12:33:11 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 6941d0d453ba -r 688a777e1b19 test-data/test4_rep2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep2.fa Tue Jan 24 12:33:11 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 6941d0d453ba -r 688a777e1b19 test-data/test4_rep3.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4_rep3.fa Tue Jan 24 12:33:11 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 6941d0d453ba -r 688a777e1b19 test-data/test5.tsv --- a/test-data/test5.tsv Tue Apr 26 15:27:37 2022 +0000 +++ b/test-data/test5.tsv Tue Jan 24 12:33:11 2023 +0000 |
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| @@ -0,0 +1,2 @@ +Genome 2seqs.bad_read.1.with_supplementary Read Count +genome1 20 |