Mercurial > repos > dfornika > augur
changeset 1:892c6690a1e8 draft default tip
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augur_align.xml Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,47 @@ +<tool id="augur_align" name="augur align" version="@TOOL_VERSION@+galaxy0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">augur</requirement> + </requirements> + <version_command>augur --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + augur align + --nthreads \${GALAXY_SLOTS:-1} + --sequences '$sequences' + --reference-sequence '$reference_sequence' + $fill_gaps + --output 'output' + ]]></command> + <inputs> + <param name="sequences" type="data" format="fasta" label="Sequences"/> + <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence"/> + <param name="fill_gaps" type="boolean" checked="false" truevalue="--fill-gaps" falsevalue="" label="Fill Gaps"/> + </inputs> + <outputs> + <data name="pre_aligner_output" format="fasta" > + <discover_datasets pattern="output.pre_aligner.fasta" format="fasta" visible="true" /> + </data> + <data name="post_aligner_output" format="fasta" > + <discover_datasets pattern="output.post_aligner.fasta" format="fasta" visible="true" /> + </data> + <data name="log" format="text" > + <discover_datasets pattern="*.log" format="text" visible="true" /> + </data> + </outputs> + <tests> + <test> + <param name="sequences" value="augur_align_test_0_sequences.input.fasta" /> + <param name="reference_sequence" value="augur_align_test_0_reference_sequence.input.fasta" /> + <param name="fill_gaps" value="false" /> + <output name="pre_aligner_output" file="augur_align_test_0_pre_aligner_output.output.fasta" /> + <output name="post_aligner_output" file="augur_align_test_0_post_aligner_output.output.fasta" /> + </test> + </tests> + <help><![CDATA[ +Align multiple sequences from FASTA or VCF. + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augur_filter.xml Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,37 @@ +<tool id="augur_filter" name="augur filter" version="@TOOL_VERSION@+galaxy0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">augur</requirement> + </requirements> + <version_command>augur --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + augur filter + --sequences '$sequences' + --metadata '$metadata' + --exclude '$exclude' + --output '$output' + ]]></command> + <inputs> + <param name="sequences" type="data" format="fasta" label="Sequences"/> + <param name="metadata" type="data" format="tabular" label="Metadata"/> + <param name="exclude" type="data" format="tabular" label="Excluded Strains"/> + </inputs> + <outputs> + <data name="output" format="fasta" /> + </outputs> + <tests> + <test> + <param name="sequences" value="augur_filter_test_0_sequences.input.fasta" /> + <param name="metadata" value="augur_filter_test_0_metadata.input.csv" /> + <param name="exclude" value="augur_filter_test_0_excluded_strains.input.csv" /> + <output name="output" file="augur_filter_test_0_output.output.fasta" /> + </test> + </tests> + <help><![CDATA[ +Filter and subsample a sequence set. + ]]></help> + <expand macro="citations" /> +</tool>
--- a/augur_parse.xml Fri Apr 05 13:45:27 2019 -0400 +++ b/augur_parse.xml Mon Apr 08 13:27:08 2019 -0400 @@ -18,35 +18,30 @@ <inputs> <param name="sequences" type="data" format="fasta" label="Sequences"/> <param name="fields" type="text" label="Fields in fasta header"/> - <param name="separator" type="text" value="|" label="Separator in fasta header"/> + <param name="separator" type="text" value="|" label="Separator in fasta header"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + </mapping> + </sanitizer> + </param> </inputs> <outputs> - <data name="output_sequences" format="fasta" /> - <data name="output_metadata" format="tabular" /> + <data name="output_sequences" format="fasta" /> + <data name="output_metadata" format="tabular" /> </outputs> <tests> <test> - <param name="sequences" value="test_00_sequences.input.fasta" /> - <param name="fields" value="strain country year" /> - <output name="output_sequences" file="test_00_sequences.output.fasta" /> - <output name="output_metadata" file="test_00_metadata.output.fasta" /> + <param name="sequences" value="augur_parse_test_0_sequences.input.fasta" /> + <param name="fields" value="strain country year" /> + <output name="output_sequences" file="augur_parse_test_0_sequences.output.fasta" /> + <output name="output_metadata" file="augur_parse_test_0_metadata.output.csv" /> </test> </tests> <help><![CDATA[ Parse delimited fields from FASTA sequence names into a TSV and FASTA file. ]]></help> - <citations> - <citation type="bibtex"> - @article{hadfield2018nextstrain, - title={Nextstrain: real-time tracking of pathogen evolution}, - author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A}, - journal={Bioinformatics}, - volume={34}, - number={23}, - pages={4121--4123}, - year={2018}, - publisher={Oxford University Press} - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/augur_tree.xml Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,24 @@ +<tool id="augur_tree" name="augur tree" version="@TOOL_VERSION@+galaxy0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">augur</requirement> + </requirements> + <version_command>augur --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + augur tree + ]]></command> + <inputs> + </inputs> + <outputs> + </outputs> + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + ]]></help> + <expand macro="citations" /> +</tool>
--- a/macros.xml Fri Apr 05 13:45:27 2019 -0400 +++ b/macros.xml Mon Apr 08 13:27:08 2019 -0400 @@ -1,3 +1,19 @@ <macros> <token name="@TOOL_VERSION@">3.1.5</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @article{hadfield2018nextstrain, + title={Nextstrain: real-time tracking of pathogen evolution}, + author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A}, + journal={Bioinformatics}, + volume={34}, + number={23}, + pages={4121--4123}, + year={2018}, + publisher={Oxford University Press} + } + </citation> + </citations> + </xml> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_output.output.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>reference +ATTGGATC +>strain-04 +ATTCGTC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_post_aligner_output.output.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>reference +ATTGGATC +>strain-04 +ATTCGTC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_pre_aligner_output.output.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC +>reference +ATTGGATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_reference_sequence.input.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,2 @@ +>reference +ATTGGATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_sequences.input.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,8 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_align_test_0_sequences.input.fasta.ref.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC +>reference +ATTGGATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_filter_test_0_excluded_strains.input.csv Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,2 @@ +strain-02 +strain-03
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_filter_test_0_metadata.input.csv Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,5 @@ +strain,country,year +strain-01,France,2012 +strain-02,Germany,2008 +strain-03,China,2016 +strain-04,Canada,2008
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_filter_test_0_output.output.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,4 @@ +>strain-01 +ATTCGATC +>strain-04 +ATTCGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_filter_test_0_sequences.input.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,8 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_parse_test_0_metadata.output.csv Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,5 @@ +strain,country,year +strain-01,France,2012 +strain-02,Germany,2008 +strain-03,China,2016 +strain-04,Canada,2008
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_parse_test_0_sequences.input.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,8 @@ +>strain-01|France|2012 +ATTCGATC +>strain-02|Germany|2008 +ATGCGATC +>strain-03|China|2016 +ATTCCATC +>strain-04|Canada|2008 +ATTCGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/augur_parse_test_0_sequences.output.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,8 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>reference +ATTGGATC +>strain-04 +ATTCGTC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.log Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,52 @@ +inputfile = orig +5 x 8 - 7 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree (efffree=0) ... + 0 / 5 +done. + +Progressive alignment 1/2... + STEP 1 / 4 (thread 0) f STEP 2 / 4 (thread 0) d STEP 3 / 4 (thread 0) d STEP 4 / 4 (thread 0) d +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree (efffree=1) ... + 0 / 5 +done. + +Progressive alignment 2/2... + STEP 1 / 4 (thread 0) f STEP 2 / 4 (thread 0) d STEP 3 / 4 (thread 0) d STEP 4 / 4 (thread 0) d +done. + +disttbfast (nuc) Version 7.407 +alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0 +1 thread(s) + + +Strategy: + FFT-NS-2 (Fast but rough) + Progressive method (guide trees were built 2 times.) + +If unsure which option to use, try 'mafft --auto input > output'. +For more information, see 'mafft --help', 'mafft --man' and the mafft page. + +The default gap scoring scheme has been changed in version 7.110 (2013 Oct). +It tends to insert more gaps into gap-rich regions than previous versions. +To disable this change, add the --leavegappyregion option. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.post_aligner.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>reference +ATTGGATC +>strain-04 +ATTCGTC-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.pre_aligner.fasta Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,10 @@ +>strain-01 +ATTCGATC +>strain-02 +ATGCGATC +>strain-03 +ATTCCATC +>strain-04 +ATTCGTC +>reference +ATTGGATC
--- a/test-data/test_00_metadata.output.tsv Fri Apr 05 13:45:27 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -strain country year -strain-01 France 2012 -strain-02 Germany 2008 -strain-03 China 2016 -strain-04 Canada 2008