<?xml version="1.0" ?>
<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2018.4">
	<description> - Find and remove adapters in demultiplexed paired-end sequences.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  
  qiime cutadapt trim-paired --i-demultiplexed-sequences=$idemultiplexedsequences

  #if str($padapterf):
   --p-adapter-f="$padapterf"
  #end if
 
   --o-trimmed-sequences=otrimmedsequences

  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if

  #if '__sq__' in str($panywheref):
    #set $panywheref_temp = $panywheref.replace('__sq__', "'")
    #set $panywheref = $panywheref_temp
  #end if

  #if str($panywheref):
   --p-anywhere-f="$panywheref"
  #end if

  #if $poverlap:
   --p-overlap=$poverlap
  #end if

  #if '__sq__' in str($panywherer):
    #set $panywherer_temp = $panywherer.replace('__sq__', "'")
    #set $panywherer = $panywherer_temp
  #end if

  #if str($panywherer):
   --p-anywhere-r="$panywherer"
  #end if

  #if $ptimes:
   --p-times=$ptimes
  #end if

  #if $pindels:
   --p-indels
  #end if

  #if str($padapterr):
   --p-adapter-r="$padapterr"
  #end if
  
  #if $perrorrate:
   --p-error-rate=$perrorrate
  #end if
  
  #if $pmatchadapterwildcards:
   --p-match-adapter-wildcards
  #end if
  
  #set $slots = '${GALAXY_SLOTS:-4}'
   --p-cores=$slots
  
  #if str($pfrontr):
   --p-front-r="$pfrontr"
  #end if
  
  #if str($pfrontf):
   --p-front-f="$pfrontf"
  #end if
  
  #if $pmatchreadwildcards:
   --p-match-read-wildcards
  #end if
  ;

  cp otrimmedsequences.qza $otrimmedsequences 
  
  ]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>

		<param label="--p-adapter-f: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is 'framed' by a 5' and a 3' adapter, use this parameter to define a 'linked' primer - see https://cutadapt.readthedocs.io for complete details.  [optional]" name="padapterf" optional="True" type="text"/>
		<param label="--p-front-f: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read.  [optional]" name="pfrontf" optional="True" type="text"/>
		<param label="--p-anywhere-f: Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read.  [optional]" name="panywheref" optional="True" type="text"/>

		<param label="--p-adapter-r: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is 'framed' by a 5' and a 3' adapter, use this parameter to define a 'linked' primer - see https://cutadapt.readthedocs.io for complete details.  [optional]" name="padapterr" optional="True" type="text"/>
		<param label="--p-front-r: Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read.  [optional]" name="pfrontr" optional="True" type="text"/>
		<param label="--p-anywhere-r: Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read.  [optional]" name="panywherer" optional="True" type="text"/>

		<param label="--p-error-rate: Maximum allowed error rate.  [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>

		<param label="--p-indels: --p-no-indels      Allow insertions or deletions of bases when matching adapters.  [default: True]" name="pindels" checked="False" type="boolean"/>

		<param label="--p-times: Remove multiple occurrences of an adapter if it is repeated, up to `times` times. [default: 1]" name="ptimes" optional="True" type="integer" value="1"/>

		<param label="--p-overlap: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found.  [default: 3]" name="poverlap" optional="True" type="integer" value="3"/>

		<param label="--p-match-read-wildcards: --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads.  [default: False]" name="pmatchreadwildcards" checked="False" type="boolean"/>

		<param label="--p-match-adapter-wildcards: --p-no-match-adapter-wildcards Interpret IUPAC wildcards (e.g., N) in adapters.  [default: True]" name="pmatchadapterwildcards" checked="False" type="boolean"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: trimmed-sequences.qza" name="otrimmedsequences"/>
	</outputs>
	<help><![CDATA[
Find and remove adapters in demultiplexed paired-end sequences.
----------------------------------------------------------------

Search demultiplexed paired-end sequences for adapters and remove them. The
parameter descriptions in this method are adapted from the official
cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
for complete details.

Parameters
----------
demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
    The paired-end sequences to be trimmed.
adapter_f : List[Str], optional
    Sequence of an adapter ligated to the 3' end. The adapter and any
    subsequent bases are trimmed. If a `$` is appended, the adapter is only
    found if it is at the end of the read. Search in forward read. If your
    sequence of interest is "framed" by a 5' and a 3' adapter, use this
    parameter to define a "linked" primer - see
    https://cutadapt.readthedocs.io for complete details.
front_f : List[Str], optional
    Sequence of an adapter ligated to the 5' end. The adapter and any
    preceding bases are trimmed. Partial matches at the 5' end are allowed.
    If a `^` character is prepended, the adapter is only found if it is at
    the beginning of the read. Search in forward read.
anywhere_f : List[Str], optional
    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
    types of matches as described under `adapter` and `front` are allowed.
    If the first base of the read is part of the match, the behavior is as
    with `front`, otherwise as with `adapter`. This option is mostly for
    rescuing failed library preparations - do not use if you know which end
    your adapter was ligated to. Search in forward read.
adapter_r : List[Str], optional
    Sequence of an adapter ligated to the 3' end. The adapter and any
    subsequent bases are trimmed. If a `$` is appended, the adapter is only
    found if it is at the end of the read. Search in reverse read. If your
    sequence of interest is "framed" by a 5' and a 3' adapter, use this
    parameter to define a "linked" primer - see
    https://cutadapt.readthedocs.io for complete details.
front_r : List[Str], optional
    Sequence of an adapter ligated to the 5' end. The adapter and any
    preceding bases are trimmed. Partial matches at the 5' end are allowed.
    If a `^` character is prepended, the adapter is only found if it is at
    the beginning of the read. Search in reverse read.
anywhere_r : List[Str], optional
    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
    types of matches as described under `adapter` and `front` are allowed.
    If the first base of the read is part of the match, the behavior is as
    with `front`, otherwise as with `adapter`. This option is mostly for
    rescuing failed library preparations - do not use if you know which end
    your adapter was ligated to. Search in reverse read.
error_rate : Float % Range(0, 1, inclusive_end=True), optional
    Maximum allowed error rate.
indels : Bool, optional
    Allow insertions or deletions of bases when matching adapters.
times : Int % Range(1, None), optional
    Remove multiple occurrences of an adapter if it is repeated, up to
    `times` times.
overlap : Int % Range(1, None), optional
    Require at least `overlap` bases of overlap between read and adapter
    for an adapter to be found.
match_read_wildcards : Bool, optional
    Interpret IUPAC wildcards (e.g., N) in reads.
match_adapter_wildcards : Bool, optional
    Interpret IUPAC wildcards (e.g., N) in adapters.

Returns
-------
trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
    The resulting trimmed sequences.
      ]]>
	</help>
<macros>
	<import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation" />
</tool>