| Previous changeset 7:dcd43b402eb3 (2018-11-23) Next changeset 9:18aad692772a (2022-06-20) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/quasitools commit 940b463cac33438233bc7a8a1695ca6d34b31a35 |
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modified:
aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml consensus.xml distance.xml dnds.xml drmutations.xml hydra.xml quality.xml |
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added:
complexity_bam.xml complexity_fasta.xml test-data/generated.bai test-data/generated.bam test-data/generated.fasta |
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removed:
complexity.xml |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 aacoverage.xml --- a/aacoverage.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/aacoverage.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="aacoverage" name="Amino Acid Coverage" version="0.4.2"> +<tool id="aacoverage" name="Amino Acid Coverage" version="0.7.0"> <description>Builds an aa census and returns its coverage</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 callaavar.xml --- a/callaavar.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/callaavar.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="aavariants" name="Amino Acid Variants" version="0.5.1"> +<tool id="aavariants" name="Amino Acid Variants" version="0.7.0"> <description>Identifies amino acid mutations</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -48,13 +48,13 @@ <param name="min_freq" value="0.01" /> <output name="output" > <assert_contents> - <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> - <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." /> - <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." /> - <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." /> - <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." /> - <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." /> - <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." /> + <has_text_matching expression="#CHROM"/> + <has_text_matching expression="0.0779" /> + <has_text_matching expression="0.0103;CAT=.;SRVL=." /> + <has_text_matching expression="0.0163;CAT=.;SRVL=." /> + <has_text_matching expression="0.0148;CAT=.;SRVL=." /> + <has_text_matching expression="0.0234;CAT=.;SRVL=." /> + <has_text_matching expression="0.0159;CAT=.;SRVL=." /> </assert_contents> </output> </test> |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 callcodonvar.xml --- a/callcodonvar.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/callcodonvar.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="callcodonvar" name="Codon Variants" version="0.5.1"> +<tool id="callcodonvar" name="Codon Variants" version="0.7.0"> <description>Identifies codon variants and non-synonymous/synonymous mutations</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 callntvar.xml --- a/callntvar.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/callntvar.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="callntvar" name="Nucleotide Variants" version="0.5.1"> +<tool id="callntvar" name="Nucleotide Variants" version="0.7.0"> <description>Identifies nucleotide variants</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity.xml --- a/complexity.xml Fri Nov 23 15:43:16 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,52 +0,0 @@ -<tool id="complexity" name="Complexity" version="0.5.1"> - <description>measures the complexity of the quasispecies reads</description> - <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - - quasitools complexity $input_fasta > complexity.txt - - ]]></command> - <inputs> - <param name="input_fasta" type="data" format="fasta" optional="false" label="Aligned FASTA Input" /> - </inputs> - <outputs> - <data format="txt" label="Complexity" name="output_complexity" from_work_dir="complexity.txt" /> - </outputs> - - <tests> - <test> - <param name="input_fasta" value="msa.fasta" /> - <output name="output_complexity"> - <assert_contents> - <has_text text="Number of haplotypes (H) : 8" /> - <has_text text="Mutation Frequency (Mfe) : 0.75" /> - </assert_contents> - </output> - </test> - </tests> - - <help><![CDATA[ -Quasispecies Complexity -======================= - -Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity. - -The measures of complexity are taken from the following work: - -Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237. - - -]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscomplexity, - title = {quasitools complexity}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> -</tool> |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity_bam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/complexity_bam.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -0,0 +1,57 @@ +<tool id="complexity_bam" name="Complexity BAM" version="0.7.0"> + <requirements> + <requirement type="package" version="0.7.0">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' && + + quasitools complexity bam '$ref_file' '$input_bam' $k -f '$filter_size' -o output.csv + + ]]></command> + <inputs> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="input_bam" type="data" format="bam" optional="false" label="BAM file" /> + <param name="k" type="integer" label="k-mer size" value="0" min="0" /> + <param name="filter_size" type="integer" label="Filter size" value="0" min="0" /> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="ref_file" value="generated.fasta" /> + <param name="input_bam" value="generated.bam" /> + <param name="k" value="200" /> + <param name="filter_size" value="0" /> + <output name="output" > + <assert_contents> + <has_text text="Position" /> + <has_text text="0" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +Quasispecies Complexity +======================= + +Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file. + +The measures of complexity are taken from the following work: +Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237. + + +]]></help> + <citations> + <citation type="bibtex"> + @misc{GitHubquasitoolscomplexity, + title = {quasitools complexity}, + publisher = {phac-nml}, + journal = {GitHub repository}, + url = {https://github.com/phac-nml/quasitools}, + } + </citation> + </citations> +</tool> |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 complexity_fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/complexity_fasta.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -0,0 +1,51 @@ +<tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0"> + <requirements> + <requirement type="package" version="0.7.0">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + quasitools complexity fasta '$input_fasta' -o output.csv + + ]]></command> + <inputs> + <param name="input_fasta" type="data" format="fasta" optional="false" label="input file" /> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="input_fasta" value="msa.fasta" /> + <output name="output"> + <assert_contents> + <has_text text="Number of Haplotypes" /> + <has_text text="8" /> + <has_text text="0.75" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +Quasispecies Complexity +======================= + +Measure the complexity of quasispecies reads using a variety of measures. The input must be an aligned FASTA file, representing a particular reqion of quasispcies from which to measure the complexity. + +The measures of complexity are taken from the following work: + +Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237. + + +]]></help> + <citations> + <citation type="bibtex"> + @misc{GitHubquasitoolscomplexity, + title = {quasitools complexity}, + publisher = {phac-nml}, + journal = {GitHub repository}, + url = {https://github.com/phac-nml/quasitools}, + } + </citation> + </citations> +</tool> |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 consensus.xml --- a/consensus.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/consensus.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="consensus" name="Consensus Sequence" version="0.5.1"> +<tool id="consensus" name="Consensus Sequence" version="0.7.0"> <description>Generate a consensus sequence from a BAM file</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 distance.xml --- a/distance.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/distance.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="distance" name="Quasispecies Distance" version="0.5.1"> +<tool id="distance" name="Quasispecies Distance" version="0.7.0"> <description>Calculate the evolutionary distance between viral quasispecies.</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 dnds.xml --- a/dnds.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/dnds.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="dnds" name="dNdS Report" version="0.5.1"> +<tool id="dnds" name="dNdS Report" version="0.7.0"> <description>Calculate the dN/dS value for each region in a bed file</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 drmutations.xml --- a/drmutations.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/drmutations.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="drmutations" name="Drug Resistance Mutations" version="0.5.1"> +<tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0"> <description></description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 hydra.xml --- a/hydra.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/hydra.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -226,6 +226,7 @@ <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." /> </assert_contents> </output> + <output name="output_stats"> <assert_contents> <has_text text="Input Size: 25000"/> |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 quality.xml --- a/quality.xml Fri Nov 23 15:43:16 2018 -0500 +++ b/quality.xml Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="quality" name="Quality control" version="0.5.1"> +<tool id="quality" name="Quality control" version="0.7.0"> <description>Performs quality control on FASTQ reads.</description> <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> + <requirement type="package" version="0.7.0">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.bai |
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| Binary file test-data/generated.bai has changed |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.bam |
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| Binary file test-data/generated.bam has changed |
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| diff -r dcd43b402eb3 -r 9def47f3c1e4 test-data/generated.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generated.fasta Tue Aug 06 08:50:28 2019 -0400 |
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| @@ -0,0 +1,2 @@ +>reference +AAGAGCGGTGAGGAGTACTCACCTCAATAGACAAGGAGAGCTATATCGCGCAGCATCGCTTCGATATTTTGCTCCTACGCATCCACACGTTGAAAGGGCCAAATGATGGTCGCTCCACTTTCTCTCTAGAACGATCGTTATGTCGAAGTCCAAGCACTACGGGGTACTACAAGTATATTACGAGCCTACTTACCTCCAAA |