Mercurial > repos > veg > mmvc
changeset 0:a3f7993dca52 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mmvc/ commit d4006c1381bdece9d754bdfebb80efb61040d6e9-dirty
author | veg |
---|---|
date | Wed, 18 Apr 2018 16:28:28 -0400 |
parents | |
children | |
files | mmvc.xml test-data/mmvc-in1.fa |
diffstat | 2 files changed, 265 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mmvc.xml Wed Apr 18 16:28:28 2018 -0400 @@ -0,0 +1,69 @@ +<?xml version="1.0"?> +<tool id="mmvc" version="1.0.2" name="mmvc"> + <description>Multinomial mixture variant caller</description> + <requirements> + <requirement type="package" version="1.0.2">mmvc</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + </stdio> + <version_command/> + <command><![CDATA[ + mmvc -j '$json_report' -f '$filter_msa' + #if str($options.advanced) == 'advanced': + -g $options.grid_density -c $options.chain_length -b $options.burnin_fraction -t $options.target_rate -p $options.posterior_threshold + #end if + '$input_fasta' + ]]></command> + <inputs> + <param name="input_fasta" label="Input FASTA" type="data" format="fasta"/> + <conditional name="options"> + <param label="Additional options" name="advanced" type="select"> + <option value="defaults">Use defaults</option> + <option value="advanced">Specify additional parameters</option> + </param> + <when value="defaults"/> + <when value="advanced"> + <param label="GRID_DENSITY" name="grid_density" type="integer" value="10"/> + <param label="CHAIN_LENGTH" name="chain_length" type="integer" value="2000000"/> + <param label="BURNIN_FRACTION" name="burnin_fraction" type="float" value="0.5"/> + <param label="TARGET_RATE" name="target_rate" type="float" value="0.01"/> + <param label="POSTERIOR_THRESHOLD" name="posterior_threshold" type="float" value="0.95"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="json" name="json_report"/> + <data format="fasta" name="filter_msa"/> + </outputs> + <tests> + <test> + <param name="input_fasta" value="mmvc-in1.fa"/> + <param name="advanced" value="advanced"/> + <param name="chain_length" value="200"/> + <output name="json_report"> + <assert_contents> + <has_text text="variant"/> + <has_text text="weight"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +MMVC +---- +Multinomial mixture variant caller + + ]]></help> + <citations> + <citation type="bibtex"> + @UNPUBLISHED{spond, + author = "Sergei Kosakovsky Pond", + title = "HyPhy: Hypothesis Testing using Phylogenies", + year = "2000", + note = "http://hyphy.org/", + url = "http://hyphy.org/"} + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mmvc-in1.fa Wed Apr 18 16:28:28 2018 -0400 @@ -0,0 +1,196 @@ +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAATAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCARCTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGRGTATATTATGATCCA +TTAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGGTATTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTCCGGAAGTATACTGCATTCACTATACCTAGTACAAACAATGAGACACCAGGG +ATTAGATATCAATACAATGTGCTACCACAGGGCTGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTAYCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACCTATAGAAATCTGTGGACATAAAACTATAGGTACGATATTAATAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGCTTGGCTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAAACCGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCGAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAGGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGGATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCTTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAGGTAAGACAATATGAT +CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA +CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATCTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGAC------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAAATCACTCTTTGGCAACGACCCTTAGTTACAGCAAAAATAGGGGAACAGCTAATA +GAAGCCCTATTAGACACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTACCAGGG +AAATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAATATGAT +CAGATACTTATAGAAATTTGTGGGAAAAAGGCTGTAGGTACAGTGTTAGTAGGACCTACA +CCTGTCAACATAATTGGACGAAATATGTTGACTCAGATTGGGTGTACTTTAAATTTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAAGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAGAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATGGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCAGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGTATACTGCATTCACTATACCTAGTATAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAGCCCTTTAGAGCAAAAAATCCAGAGATGGTGATTTAC +CAATACATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGGCAGCATAGAACAAAA +ATACAAGAGTTGAGAGAACATCTACTGAAGTGGGGATTAACCACACCAGATAAAAAACAT +CAGAAAGAACCTCCATTTCTTTGGATGGGATATGAACTCCATCCTGACAAATGGACAGTC +CAGCCTATAAAGCTGCCAGAAAAAGACAGCTGGACTGTCAATGATATACAGAAATTAGTG +GGAAAGCTAAATTGGGCAAGTCAGATTTATGCAGGAATTAAAGTAAGGCAACTGTGTAAA +CTCCTCAGGGGAGCCAAAGCACTAACAGAGATAGTAACACTGACTGAGGAAGCAGAATTA +GAATTAGCAGAAAACAGAGAAATTCTAAAAGAACCTGTTCATGGAGTATATTATGATCCA +TCAAAAGACCTAGTAGCAGAAATACAGAAACAAGGGCAAGACCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATTTAAAAACAGGAAAATATGCAAAAAAGAAGTCTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGTAGTGCAAAAGGTGTCTACAGAAAGCATAGTA +ATATGGGGAAAGACCCCTAAATTTAGACTACCCATACAAAAAGAAACATGGGAAGCA--- +------------------------------------------------------------ +--------------------------------------------------------- +>Z|JP|K03455|2036|DUPLICATE +CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAG +GAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGA +AGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGAT +CAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA +CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCC +ATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATG +GAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT +GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAAT +AAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAA +AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGAT +GAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAA +AGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTAT +CAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAA +ATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT +CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTA +CAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTG +GGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAA +CTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA +GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCA +TCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATT +TATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCAC +ACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTA +ATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGG +TGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCC +TTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTC +>Z|JP|K03455|2036 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------AAATATGTTGACTCAGATTGGTTGTACTTTAAATTTTCCA +ATTAGTCCTATTGAAACTGTACCAGTAAAATTGAAGCCAGGAATGGATGGCCCAAGGGTT +AAACAATGGCCATTGACAGAAGAAAAAATAAAGGCGTTAACAGAAATTTGTACAGAAATG +GAAAGGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAATATTT +GCCATAAAGAAAAAAGATAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTCAAT +AAAAGAACTCAAGACTTCTGGGAGGTCCAACTAGGAATACCTCATCCCGCGGGATTAAAA +AAGAAAAAATCAGTAACAGTACTAGATGTGGGGGATGCATATTTTTCAGTTCCCTTAGAT +AAAGACTTTAGAAAGCATACTGCATTCACTATACCTAGTGTAAATAATGAAACACCGGGG +ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTTCAG +GCTAGCATGACAAAAATCTTAGAACCCTTTAGAACAAACAATCCAGAGATGGTGATTTAC +CAATATATGGATGATTTATATGTAGGATCTGACTTAGAGATAGGACAGCATAGAGAAAAA +ATACAGGAGTTGAGAGAACATCTACTGAAATGGGGATTTACCACACCAGATAAAAAA--- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------------------------------------