comparison mothur/tools/mothur/filter.seqs.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

<tool id="mothur_filter_seqs" name="Filter.seqs" version="1.19.0" force_history_refresh="True">
 <description>removes columns from alignments</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='filter.seqs'

  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="filter" name="out_filter" label="${tool.name} on ${on_string}: filter" />
  <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs. 

.. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs


 </help>
</tool>

35:95d75b35e4d2

<tool id="mothur_filter_seqs" name="Filter.seqs" version="1.20.0" force_history_refresh="True">
 <description>removes columns from alignments</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='filter.seqs'

  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="filter" name="out_filter" label="${tool.name} on ${on_string}: filter" />
  <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs. 

.. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs

v.1.20.0: Updated to Mothur 1.33


 </help>
</tool>