| Previous changeset 1:1abf6b32ecfd (2017-12-13) Next changeset 3:8dacd75ca8f1 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/quasitools commit de4309426401ce655435d6867b05c3673b9d086f |
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modified:
aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml consensus.xml dnds.xml drmutations.xml hydra.xml |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 aacoverage.xml --- a/aacoverage.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/aacoverage.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="aacoverage" name="Amino Acid Coverage" version="0.1.0"> <description>Builds an aa census and returns its coverage</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 callaavar.xml --- a/callaavar.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/callaavar.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="aavariants" name="Amino Acid Variants" version="0.1.0"> <description>Identifies amino acid mutations</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 callcodonvar.xml --- a/callcodonvar.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/callcodonvar.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="callcodonvar" name="Codon Variants" version="0.1.0"> <description>Identifies codon variants and non-synonymous/synonymous mutations</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -53,4 +53,4 @@ ]]></help> <citations> </citations> -</tool> \ No newline at end of file +</tool> |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 callntvar.xml --- a/callntvar.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/callntvar.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="callntvar" name="Nucleotide Variants" version="0.1.0"> <description>Identifies nucleotide variants</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 consensus.xml --- a/consensus.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/consensus.xml Mon Mar 26 14:23:30 2018 -0400 |
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| b'@@ -1,15 +1,21 @@\n-<tool id="consensus" name="Consensus Sequence" version="0.1.0">\n+<tool id="consensus" name="Consensus Sequence" version="0.2.0">\n <description>Generate a consensus sequence from a BAM file</description>\n <requirements>\n- <requirement type="package" version="0.2.2">quasitools</requirement>\n+ <requirement type="package" version="0.2.3">quasitools</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n \n ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&\n- quasitools consensus $input_bam $ref_file \n+ quasitools consensus $input_bam $ref_file \n+\n+ #if $fasta_id.type == \'default\':\n+ -i $input_bam.name \n+ #elif $fasta_id.type == \'custom\':\n+ -i $fasta_id.custom_id \n+ #end if\n \n #if $base_type.type == \'mixed\':\n- -p $base_type.percentage \n+ -p $base_type.percentage \n #end if\n \n -o output.fasta\n@@ -29,6 +35,17 @@\n <param name="percentage" type="integer" min="0" max="100" optional="true" value="100" label="Percentage" help="Percentage to include base in mixture. Defaults to 100."/>\n </when>\n </conditional>\n+ <conditional name="fasta_id">\n+ <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">\n+ <option value="default" >Use bam dataset name</option>\n+ <option value="custom">Use custom name</option>\n+ </param>\n+ <when value="default">\n+ </when>\n+ <when value="custom">\n+ <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>\n+ </when>\n+ </conditional>\n </inputs>\n <outputs>\n <data format="fasta" name="output" from_work_dir="output.fasta" />\n@@ -40,7 +57,7 @@\n <param name="type" value="majority" />\n <output name="output" >\n <assert_contents>\n- <has_text text=">blah_100_hxb2_pol" />\n+ <has_text text=">align.bam_100_hxb2_pol" />\n <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGA'..b'TGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGAT" />\n </assert_contents>\n </output>\n@@ -52,7 +69,7 @@\n <param name="percentage" value="5" />\n <output name="output" >\n <assert_contents>\n- <has_text text=">blah_5_hxb2_pol" />\n+ <has_text text=">align.bam_5_hxb2_pol" />\n <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAMAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGAT" />\n </assert_contents>\n </output>\n' |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 dnds.xml --- a/dnds.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/dnds.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="dnds" name="dNdS Report" version="0.1.0"> <description>Calculate the dN/dS value for each region in a bed file</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -38,4 +38,4 @@ ]]></help> <citations> </citations> -</tool> \ No newline at end of file +</tool> |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 drmutations.xml --- a/drmutations.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/drmutations.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0"> <description></description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r 1abf6b32ecfd -r a7093d5933a8 hydra.xml --- a/hydra.xml Wed Dec 13 10:28:31 2017 -0500 +++ b/hydra.xml Mon Mar 26 14:23:30 2018 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="hydra" name="Hydra pipeline" version="0.1.0"> <description>Identifies drug resistance within an NGS dataset</description> <requirements> - <requirement type="package" version="0.2.2">quasitools</requirement> + <requirement type="package" version="0.2.3">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -95,7 +95,7 @@ </conditional> <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." /> - <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." /> + <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." /> <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." /> <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/> @@ -115,6 +115,9 @@ <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> + <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta"> + <filter>generate_consensus</filter> + </data> </outputs> <tests> <test> |