comparison mothur/README @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

6:ce6e81622c6a

Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 

Install mothur v.1.19.0 on your galaxy system so galaxy can execute the mothur command
  ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions )
  http://www.mothur.org/wiki/Download_mothur
  http://www.mothur.org/wiki/Installation
  ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )

    <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
      <tool file="mothur/sffinfo.xml"/>
      <tool file="mothur/make.fastq.xml"/>
      <tool file="mothur/fastq.info.xml"/>
      <tool file="mothur/summary.seqs.xml"/>
      <tool file="mothur/reverse.seqs.xml"/>
      <tool file="mothur/list.seqs.xml"/>
      <tool file="mothur/get.seqs.xml"/>
      <tool file="mothur/remove.seqs.xml"/>
      <tool file="mothur/trim.seqs.xml"/>

      <tool file="mothur/chimera.bellerophon.xml"/>
      <tool file="mothur/chimera.ccode.xml"/>
      <tool file="mothur/chimera.check.xml"/>
      <tool file="mothur/chimera.pintail.xml"/>
      <tool file="mothur/chimera.slayer.xml"/>
    <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
      <tool file="mothur/pre.cluster.xml"/>
      <tool file="mothur/cluster.fragments.xml"/>
      <tool file="mothur/cluster.xml"/>
      <tool file="mothur/hcluster.xml"/>

      <tool file="mothur/remove.lineage.xml"/>
      <tool file="mothur/phylotype.xml"/>
      <tool file="mothur/phylo.diversity.xml"/>
      <tool file="mothur/clearcut.xml"/>
      <tool file="mothur/indicator.xml"/>
      <tool file="mothur/TreeVector.xml"/>
  </section> <!-- metagenomics_mothur -->


############ DESIGN NOTES #########################################################################################################
Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py

* Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
* Many mothur commands require date to be read into memory (using read.dist, read.otu, read.tree) before executed the command,  
  these are accomplished in the tool_config and mothur_wrapper.py with --READ_cmd= and --READ_<option> parameters. 
* Every tool will produce the logfile of the mothur run as an output.
* When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
* When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 
  are included in the --new_datasets parameter to mothur_wrapper.py
 

 # specifies files to copy to the new_file_path
 # The list is separated by commas
 # Each item  conatins:   a regex pattern for matching filenames and  a galaxy datatype (separated by :)
 # The regex match.groups()[0] is used as the id name of the dataset, and must result in  unique name for each output
 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
 # Many mothur commands first require data to be read into memory using: read.otu, read.dist, or read.tree
 # This prequisite command and its params are prefixed with 'READ_'
 --READ_cmd='read.otu'
 --READ_list=/home/galaxy/data/database/files/001/dataset_1557.dat
 --READ_group='/home/galaxy/data/database/files/001/dataset_1545.dat'
 --READ_label='unique,0.07'

7:7bfe1f843858

Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 

Install mothur v.1.20.0 on your galaxy system so galaxy can execute the mothur command
  ( This version of wrappers is designed for Mothur version 1.19 - it may work on later versions )
  http://www.mothur.org/wiki/Download_mothur
  http://www.mothur.org/wiki/Installation
  ( This Galaxy Mothur wrapper will invoke Mothur in command line mode: http://www.mothur.org/wiki/Command_line_mode )

    <label text="Mothur Sequence Analysis" id="mothur_sequence_analysis"/>
      <tool file="mothur/sffinfo.xml"/>
      <tool file="mothur/make.fastq.xml"/>
      <tool file="mothur/fastq.info.xml"/>
      <tool file="mothur/summary.seqs.xml"/>
      <tool file="mothur/count.seqs.xml"/>
      <tool file="mothur/reverse.seqs.xml"/>
      <tool file="mothur/list.seqs.xml"/>
      <tool file="mothur/get.seqs.xml"/>
      <tool file="mothur/remove.seqs.xml"/>
      <tool file="mothur/trim.seqs.xml"/>

      <tool file="mothur/chimera.bellerophon.xml"/>
      <tool file="mothur/chimera.ccode.xml"/>
      <tool file="mothur/chimera.check.xml"/>
      <tool file="mothur/chimera.pintail.xml"/>
      <tool file="mothur/chimera.slayer.xml"/>
      <tool file="mothur/chimera.uchime.xml"/>
    <label text="Mothur Operational Taxonomy Unit" id="mothur_taxonomy_unit"/>
      <tool file="mothur/pre.cluster.xml"/>
      <tool file="mothur/cluster.fragments.xml"/>
      <tool file="mothur/cluster.xml"/>
      <tool file="mothur/hcluster.xml"/>

      <tool file="mothur/remove.lineage.xml"/>
      <tool file="mothur/phylotype.xml"/>
      <tool file="mothur/phylo.diversity.xml"/>
      <tool file="mothur/clearcut.xml"/>
      <tool file="mothur/indicator.xml"/>
      <tool file="mothur/deunique.tree.xml"/>
      <tool file="mothur/TreeVector.xml"/>
  </section> <!-- metagenomics_mothur -->


############ DESIGN NOTES #########################################################################################################
Each mothur command has it's own tool_config (.xml) file, but all call the same python wrapper code: mothur_wrapper.py

* Every mothur tool will call mothur_wrapper.py script with a --cmd= parameter that gives the mothur command name.
* Every tool will produce the logfile of the mothur run as an output.
* When the outputs of a mothur command could be determined in advance, they are included in the --result= parameter to mothur_wrapper.py
* When the number of outputs cannot be determined in advance, the name patterns and datatypes of the ouputs 
  are included in the --new_datasets parameter to mothur_wrapper.py
 

 # specifies files to copy to the new_file_path
 # The list is separated by commas
 # Each item  conatins:   a regex pattern for matching filenames and  a galaxy datatype (separated by :)
 # The regex match.groups()[0] is used as the id name of the dataset, and must result in  unique name for each output
 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'

 ## 
 ## NOTE:   The "read" commands were eliminated with Mothur version 1.18
 ##