Mercurial > repos > dcorreia > phylogeny_tools
changeset 42:819529b8d1f3 draft
planemo upload commit c85f6d1b96277d10e4362709ea16fe07bb0cfc9e
| author | dcorreia |
|---|---|
| date | Tue, 15 Nov 2016 03:07:11 -0500 |
| parents | b00618525fd7 |
| children | ed2407cb8c10 |
| files | clustalo/clustalo.xml fasta2phylip/fasta_to_phylip.xml fastme_oneclick/fastme_oneclick.xml gblock/gblocks.xml gblock/gblocks_onclick.xml muscle/muscle.xml muscle/test-data/seqtest_aln.fasta noisy_oneclick/noisy_oneclick.xml phyml-sms_oneclick/phyml_sms_oneclick.xml phyml_oneclick/phyml_oneclick.xml seqtypedetect/seqtypedetect.xml tool_dependencies.xml |
| diffstat | 12 files changed, 142 insertions(+), 81 deletions(-) [+] |
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--- a/clustalo/clustalo.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/clustalo/clustalo.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,9 @@ <tool id="clustalo" name="Clustal Omega" version="1.2.1.1"> <description>Multiple sequence alignment software</description> + <edam_operations> + <edam_operation>operation_0499</edam_operation> + <edam_operation>operation_0492</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="1.2.1">clustalo</requirement> </requirements>
--- a/fasta2phylip/fasta_to_phylip.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/fasta2phylip/fasta_to_phylip.xml Tue Nov 15 03:07:11 2016 -0500 @@ -9,7 +9,7 @@ <inputs> <param name="input" format="fasta" type="data" label="Source file" help="fasta or phylip format"/> <param name="format" type="select" label="format" help="Sequencial: sequences are one one line"> - <option value="">Interleave</option> + <option value="--interleave">Interleave</option> <option value="--sequencial">Sequencial</option> </param> </inputs>
--- a/fastme_oneclick/fastme_oneclick.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/fastme_oneclick/fastme_oneclick.xml Tue Nov 15 03:07:11 2016 -0500 @@ -6,7 +6,6 @@ </edam_operations> <requirements> <requirement type="package" version="2.1.5">fastme</requirement> - <requirement type="seqtypedetect" version="1.0">seqtypedetect</requirement> </requirements> <version_command> <![CDATA[ fastme --version ]]> @@ -15,65 +14,101 @@ <exit_code range="1:" level="fatal" /> </stdio> <command> - fastme --input_data=$input - --output_tree=$outputTree - --output_matrix=$outputMatrix - --output_info=$outputLog - --nb_threads=\${GALAXY_SLOTS:-1} + <![CDATA[ + fastme + --input_data=$input + --output_tree=$outputTree + --output_matrix=$outputMatrix + --output_info=$outputLog + --nb_threads=\${GALAXY_SLOTS:-1} - #if $typeChoice.datatype =="d" - --dna=$typeChoice.modeldna + #if ($usetree.inputTree == "true"): + --user_tree=${$usetree.userInputTree.name} + #end if - #else if $typeChoice.datatype =="p" - --protein=$typeChoice.modelprot + #if $typeChoice.datatype =="d" + --dna=$typeChoice.modeldna + + #else if $typeChoice.datatype =="p" + --protein=$typeChoice.modelprot - #else if $typeChoice.datatype =="cfg": - ## Read information of sequence type - ## read an info file to choose which option set and set a model by default - #set $info = open( str($input_info) ).read() - #if 'dna' in $info: - --dna=T - #else if 'protein' in $info: - --protein=L - #end if - #end if + #else if $typeChoice.datatype =="cfg": + ## Read information of sequence type + ## read an info file to choose which option set and set a model by default + #set $info = open( str($input_info) ).read() + #if 'dna' in $info: + --dna=T + #else if 'protein' in $info: + --protein=L + #end if - #if $gammaChoice.gamma == "true" - --gamma=$gammaChoice.rate - #end if + #end if - $distance - $equilibrium - $removeGap - $treeRefinement - -f $supportPrecision + #if $gammaChoice.gamma == "true" + --gamma=$gammaChoice.rate + #end if - #if $bootChoice.boot == "true" - --output_boot=$outputBoostrap - --bootstrap=$bootChoice.replicates - #end if + $distance + $equilibrium + $removeGap + $treeRefinement + -f $supportPrecision - >> tmp_stdout; + #if $bootChoice.boot == "true" + --output_boot=$outputBoostrap + --bootstrap=$bootChoice.replicates + #end if - cat tmp_stdout > $outputLog; - + >> tmp_stdout; + cat tmp_stdout > $outputLog; + ]]> </command> <inputs> <param name="input" type="data" format="phylip, phy" label="Fastme input" help="Phylip Alignment or Matrix file"/> + <conditional name="usetree"> + <param name="inputTree" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use input tree guide" /> + <when value="true"> + <param name="userInputTree" type="data" label="Tree file" help="newick format"/> + </when> + <when value="false"/> + </conditional> <param name="fileout_label" type="text" value="Newick tree" label="Output name" help="Output name for files" /> <conditional name="typeChoice"> - <param name="seqtype" type="select" display="radio" label="Sequence type" > + <param name="datatype" type="select" display="radio" label="Data type" > <option value="d">DNA</option> <option value="p">Protein</option> <option value="m">Matrix</option> - <option value="auto">Automatic detection</option> <option value="cfg">Information file</option> </param> - <when value="auto"> - <param name="input_info" format="txt" type="data" hidden="True"/> + <when value="d"> + <param name="modeldna" type="select" label="Evolutionary model"> + <option value="4">F84</option> + <option value="R">RY</option> + <option value="1">F81</option> + <option value="J">JC69</option> + <option value="K">K2P</option> + <option value="T" selected="true">TN93</option> + <option value="p">p-distance</option> + </param> </when> + <when value="p"> + <param name="modelprot" type="select" label="Evolutionary model"> + <option value="L">LG</option> + <option value="W">WAG</option> + <option value="J">JTT</option> + <option value="h">Day off</option> + <option value="C">CpRev</option> + <option value="D">DCMut</option> + <option value="b">HIVb</option> + <option value="I">HIVw</option> + <option value="M">MtREV</option> + <option value="R">RtREV</option> + <option value="p">p-distance</option> + </param> + </when> + <when value="m"/> <when value="cfg"> - <param name="input_info" format="txt" type="data" multiple="false" label="Config file" help="Precompute file containning sequence description (dna or protein)"/> + <param name="input_info" format="txt" type="data" multiple="false" label="Config file" help="Precompute file containning sequence description (dna or protein)"/> </when> </conditional> <param name="equilibrium" type="boolean" label="Equilibrium frequencies" truevalue="--equilibrium" falsevalue="" help="By default, frequencies are globally counted from the nucleotides alignment or defined by the proteic substitution model. By checking the box, frequencies are pairwise estimated by counting the nucleotides or estimated by counting the amino-acids in the alignment."/> @@ -123,7 +158,7 @@ <data name="outputBoostrap" format="nwk" label="FastME Bootstrap trees"> <filter>bootChoice['boot'] == "true"</filter> </data> - <data name="outputMatrix" format="phylip.dist" label="FastME Distance matrix"/> + <data name="outputMatrix" format="txt" label="FastME Distance matrix"/> </outputs> <tests> <test>
--- a/gblock/gblocks.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/gblock/gblocks.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,8 @@ <tool id="gblocks" name="Gblocks" version="0.91.1"> <description>cleaning aligned sequences</description> + <edam_operations> + <edam_operation>operation_0368</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="0.91b">gblocks</requirement> </requirements>
--- a/gblock/gblocks_onclick.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/gblock/gblocks_onclick.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,8 @@ <tool id="gblocks_oneclick" name="Gblocks OneClick" version="0.91.1"> <description>cleaning aligned sequences</description> + <edam_operations> + <edam_operation>operation_0368</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="0.91b">gblocks</requirement> </requirements> @@ -44,7 +47,7 @@ <when value="-t=c"/> <when value="-t=p"/> <when value="cfg"> - <param name="input_info" format="txt" type="data" multiple="false" label="Config file" + <param name="input_info" format="txt" type="data" multiple="false" label="Information file" help="Precompute file containning sequence description (dna or protein)"/> </when> </conditional>
--- a/muscle/muscle.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/muscle/muscle.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,8 @@ <tool id="muscle" name="MUSCLE" version="3.8.31.1"> <description>MUltiple Sequence Comparison by Log- Expectation</description> + <edam_operations> + <edam_operation>operation_0492</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="3.8.31">muscle</requirement> </requirements>
--- a/muscle/test-data/seqtest_aln.fasta Tue Nov 08 12:18:28 2016 -0500 +++ b/muscle/test-data/seqtest_aln.fasta Tue Nov 15 03:07:11 2016 -0500 @@ -1,40 +1,40 @@ >TestSequence1 ERNECFLKHKDDDPNLPPVVKPEPEALCTAFQENNNKFLENYLYEVARRHPYFYGPELLY -YV--KQYKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGER -AA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLAK -YVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNYK -EAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDELQ -PLVDEPQL-LKLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMGN -KCCTLPESKR--- +-YVKQ--YKAILTECCQAACCQAADKATCLAPKAKVLKEKLLASSAKQRHKCASIQKFGE +RAA-----AFKAWSIARLSQRFPKADFMDLSKLVTDLSKIHKECCHGDLLECADDREDLA +KYVQDVCASFSSKLKECCDKPLLEKSHCISELENDDLPNDLPSITTDFVEDKDVCKLLNY +KEAKDVFL--GTFLYEYSRRHPEYAVSLLLRIAKGYEATLERCCATDDAHACYSKVFDEL +QPLVDEPQLL-KLMKRNCELFENLGAYGFQNALIIRYTKKMPQVSTPTLLVISKELANMG +NKCCTLPESKR--- >TestSequence2 ERADCFASHRDDNPGFPLMVRPPVDELCASYQADAQMFAGKYLYEVARRYPYFYAPELLY -YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGER -HGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELGK -YMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NYA -EAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDELK -PLIDEPDE-LNLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVGT -KCCSLAEGERVCA +-YAQKLLYKDALAEC-----CSAADKAACLTPKIDDLKESVMTSGAKQRFKCAGIEKFGE +RHGDLC--AFKAWAVARLSQKFPNADFAEISKIVTDLTKINKECCHGDLLECADDRVELG +KYMCDNKDSISSKLGKCCEKPLLEKGHCIAELERDDMPADLSPIEADFVEDKEVCK--NY +AEAKDVFLVCGTFLYELSRRHPEYSVVMLLRLAKGYEAVLEKCCATGDPPACYAKVFDEL +KPLIDEPDEL-NLVKHNCELYGNLQEYGFQNALLIRYTKKMPQ---PTLVEVSRNLGKVG +TKCCSLAEGERVCA >TestSequence3 ERNECFLSHKDDSPDLPKL-KPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLY -AY-ANKYNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGER -HGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAK -YICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NYQ -EAKDAFLVCGSFLYEYSRRHPE-YVLLRLALLKEYEATLEECCAKDDPHACYSTVFDKLK -HLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGT -RCCTKPESER--- +AYANK--YNGVFQEC-----CQAEDKGACLLPKIETMREKVLTSSARQRLRCASIQKFGE +RHGDLVCAALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLA +KYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAVPENLPPLTADFAEDKDVCK--NY +QEAKDAFLVCGSFLYEYSRRHPEY-VLLRLALLKEYEATLEECCAKDDPHACYSTVFDKL +KHLVDEPQVFLNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVG +TRCCTKPESER--- >TestSequence4 ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF --F-AKRYKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGER -HGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAK -YICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NYA -EAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFK -PLVEEPQL-LNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGS -KCCKHPEAKR--- +-FAKR--YKAAFTEC-----CQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGE +RHGDLVCAAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLA +KYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCK--NY +AEAKDVFLVCGMFLYEYARRHPRESVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEF +KPLVEEPQLL-NLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVG +SKCCKHPEAKR--- >TestSequence5 ERNECFLQHKDDNPGFGQLVTPEADAMCTAFHENEQRFLGKYLYEIARRHPYFYAPELLY --Y-AEEYKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGER -HGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLAK -YICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NYQ -EAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEFK -PLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVGS -KCCTHPEAER--- +-YAEE--YKGVFTEC-----CEAADKAACLTPKVDALREKVLASSAKERLKCASLQKFGE +RHGDLVFLAFKAWSVARLSQKFPKAEFAEISKLVTDLAKIHKECCHGDLLECADDRADLA +KYICENQDSISTKLKECCGKPVLEKSHCISEVERDELPADLPPLAVDFVEDKEVCK--NY +QEAKDVFLVCGTFLYEYSRRHPS-SVSLLLRLAKEYEATLEKCCATDDPPACYAHVFDEF +KPLVEEPHNQDNLVKTNCELFEKLGEYGFQNALLVRYTKKVPQVSTPTLVEVSRSLGKVG +SKCCTHPEAER---
--- a/noisy_oneclick/noisy_oneclick.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/noisy_oneclick/noisy_oneclick.xml Tue Nov 15 03:07:11 2016 -0500 @@ -61,8 +61,8 @@ <when value="D"></when> <when value="P"></when> <when value="R"></when> - <when value="auto"> - <param name="input_info" type="data" format="txt" label="info" help="Precompute file containning sequence description (dna or protein)" /> + <when value="cfg"> + <param name="input_info" type="data" format="txt" label="Information file" help="Precompute file containning sequence description (dna or protein)" /> </when> </conditional> <param name="cutoff" type="float" value="0.8" min="0" max="1" label="cut-off [ 0-1 ]" help="Columns with a score below FLOAT are removed from the output alignment." /> @@ -94,7 +94,7 @@ </param> <when value="nnet"/> <when value="qnet"/> - <option value="all"/> + <when value="all"/> <when value="rand"> <param name="randpermut" type="integer" value="1000" label="random permutation"/> </when>
--- a/phyml-sms_oneclick/phyml_sms_oneclick.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/phyml-sms_oneclick/phyml_sms_oneclick.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,8 +1,12 @@ <tool id="phyml-sms_oneclick" name="PhyML-SMS OneClick" version="1.3.1"> - <description>Maximum likelihood-based inference of phylogenetic trees with Smart Model Selection</description> + <description>Maximum likelihood-based inference of phylogenetic trees with Smart Model Selection</description> + <edam_operations> + <edam_operation>operation_0540</edam_operation> + <edam_operation>operation_0324</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="1.3">phyml-sms</requirement> - <requirement type="package" version="3.0.1">R</requirement> + <requirement type="package" version="3.0.1">R</requirement> </requirements> <command><![CDATA[ @@ -62,7 +66,7 @@ <when value="nt" /> <when value="aa" /> <when value="cfg"> - <param name="input_info" format="txt" type="data" multiple="false" label="Config file" help="Precompute file containning sequence description (dna or protein)"/> + <param name="input_info" format="txt" type="data" multiple="false" label="Information file" help="Precompute file containning sequence description (dna or protein)"/> </when> </conditional> <param name="stat_crit" type="select" label="Statistical criterion to select the model"> @@ -85,6 +89,7 @@ <when value="boot"> <param type="integer" name="boot_number" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer"/> </when> + <when value="no"/> </conditional> <conditional name="inpuTree"> <param name="inputtree" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use input starting tree" />
--- a/phyml_oneclick/phyml_oneclick.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/phyml_oneclick/phyml_oneclick.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,9 @@ <tool id="phyml_oneclick" name="PhyML Oneclick" version="3.1"> <description>Phylogeny software based on the maximum-likelihood</description> + <edam_operations> + <edam_operation>operation_0540</edam_operation> + <edam_operation>operation_0324</edam_operation> + </edam_operations> <requirements> <requirement type="package" version="3.1">phyml</requirement> </requirements> @@ -172,7 +176,7 @@ </conditional> </inputs> <outputs> - <data name="output_tree" format="txt" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" /> + <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" /> <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/> <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/> </outputs>
--- a/seqtypedetect/seqtypedetect.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/seqtypedetect/seqtypedetect.xml Tue Nov 15 03:07:11 2016 -0500 @@ -1,5 +1,6 @@ <tool id="seqtypedetect" name="Sequence type detection" version="1.0"> <description>Detect sequence datatype on fasta file</description> + <command interpreter="python"> <![CDATA[ seqtypedetect.py $input 2>&1 1>$output
--- a/tool_dependencies.xml Tue Nov 08 12:18:28 2016 -0500 +++ b/tool_dependencies.xml Tue Nov 15 03:07:11 2016 -0500 @@ -4,7 +4,7 @@ <repository changeset_revision="8e1916ccca9a" name="package_clustalo_1_2_1" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="gblocks" version="0.91b"> - <repository changeset_revision="42c0927e0ce6" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="cc74017fbc04" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="muscle" version="3.8.31"> <repository changeset_revision="17c53de3f872" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> @@ -12,6 +12,9 @@ <package name="phyml-sms" version="1.3"> <repository changeset_revision="244d490a5cf5" name="package_phyml_sms_1_3" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="phyml" version="3.1"> + <repository changeset_revision="48b0369fdb5b" name="package_phyml_3_1" owner="vlefort" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="R" version="3.0.1"> <repository changeset_revision="55b8ae401f5c" name="package_r_3_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>