annotate uclust2otutable.xml @ 0:e85e7ba38aff draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/uc2otutable commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e-dirty"

<tool id="uclust2otutable" name="OTUTable" version="1.0.0">
  <description>Convert UCLUST format from Vsearch to OTU Table</description>
  <version_command>
	python ${__tool_directory__}/uclust2otutable.py --version
  </version_command>
  <command detect_errors="aggressive">
    python ${__tool_directory__}/uclust2otutable.py 
	-i '$inputfile' 
	-o '$output'
  </command>
  <inputs>
    <param format="tabular" name="inputfile" type="data" label="UCLUST from Vsearch" />
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="OTU_TABLE_${inputfile.display_name}"/>
  </outputs>
  <tests>
    <test>
      <param name="inputfile" value="uc_input.txt"/>
      <output name="output" file="uc_output.txt"/>
    </test>
  </tests>

  <help>
** what it does **

Converts UCLUST format (.uc) output from Vsearch search into raw count table. The description of UCLUST format is based on the information that can be found on UCLUST_ documentation page.

.. _UCLUST: http://www.drive5.com/uclust/uclust_userguide_1_1_579.html

--------

=======
Example
=======
    
Some example records:
---------------------

==== ======= ==== ==== ====== === === ========= ========== ======
Type Cluster Size %Id  Strand Qlo Tlo Alignment Query      Target
---- ------- ---- ---- ------ --- --- --------- ---------- ------
   S       0  292  '*'   '*'  '*' '*'    '*'    AH70_12410  '*'
   H       0  292 99.7   '+'   0   0     292M   AH70_12410  '*'
   S       0  292  '*'   '*'  '*' '*'    '*'    AH70_12410  '*'
   H       0  292 98.2   '+'   0   0     292M   AH70_12410  '*'
==== ======= ==== ==== ====== === === ========= ========== ======

Each record has ten fields, separated by tabs:
----------------------------------------------

========= ===========================================
Column    Description
--------- -------------------------------------------
Type      Record type
Cluster   Cluster number
Size      Sequence length or cluster size
%Id       Identity to the seed(as a percentage), or * if this is a seed.
Strand    '+' plus strand, '-' minus strand, or '.' amino acids.
Qlo       0-based coordinate of alignment start in the query sequence.
Tlo       0-based coordinate of alignment start in target (seed) sequence. If minus strand, Tlo is relative to start of reverse-complement target.
Alignment Compressed representation of alignment to the seed(see below), or '*' if a seed.
Query     FASTA label of query sequence
Target    FASTA label of target(seed / library / database) sequence. or '*' if a seed.
========= ===========================================

Record Types are:
-----------------

====== ===========================================
Column Description
------ -------------------------------------------
L      Library seed(generated only if a match if found to this seed).
S      New seed.
H      Hit, also known as an accept; i.e. a successful match.
D      Library cluster.
C      New cluster.
N      Not matched (a sequence that didn't match library with --libonly specified).
R      Reject (generated only if --output_rejects is specified)
====== ===========================================

The alignment is compressed using run-length encoding, as follows. Each column in the alignment is classified as M,D or I:
--------------------------------------------------------------------------------------------------------------------------

==== ====== ============== =============
Code Name   Query sequence Seed sequence
---- ------ -------------- -------------
M    Match  Letter         Letter
D    Delete Gap            Letter
I    Insert Letter         Gap
==== ====== ============== =============

--------


  </help>

</tool>