view mothur/tools/mothur/fastq.info.xml @ 32:ec8df51e841a

Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation

<tool id="mothur_fastq_info" name="Fastq.info" version="1.24.0">
 <description>Convert fastq to fasta and quality</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='fastq.info'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile
  --outputdir='$logfile.extra_files_path'
  --fastq=$fastq
 </command>
 <inputs>
  <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>
  <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" />
  <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta">
   <filter>fasta == True</filter>
  </data>
  <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual">
   <filter>qfile == True</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team 
in the Department of Microbiology and Immunology at The University of Michigan,  
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The fastq.info_ command reads a fastq file and creates a fasta and quality file.


.. _fastq.info: http://www.mothur.org/wiki/Fastq.info

 </help>
</tool>