view qiime2-2020.8/qiime_cutadapt_trim-single.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
      version="2020.8">
  <description>Find and remove adapters in demultiplexed single-end sequences.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime cutadapt trim-single

--i-demultiplexed-sequences=$idemultiplexedsequences

--p-cores=$pcores

#if $padapter:
 --p-adapter
#end if

#if str($pfront):
  --p-front=$pfront
#end if
#if '__ob__' in str($panywhere):
  #set $panywhere_temp = $panywhere.replace('__ob__', '[')
  #set $panywhere = $panywhere_temp
#end if
#if '__cb__' in str($panywhere):
  #set $panywhere_temp = $panywhere.replace('__cb__', ']')
  #set $panywhere = $panywhere_temp
#end if
#if 'X' in str($panywhere):
  #set $panywhere_temp = $panywhere.replace('X', '\\')
  #set $panywhere = $panywhere_temp
#end if
#if '__sq__' in str($panywhere):
  #set $panywhere_temp = $panywhere.replace('__sq__', "'")
  #set $panywhere = $panywhere_temp
#end if
#if '__db__' in str($panywhere):
  #set $panywhere_temp = $panywhere.replace('__db__', '"')
  #set $panywhere = $panywhere_temp
#end if

#if str($panywhere):
  --p-anywhere=$panywhere
#end if

--p-error-rate=$perrorrate

#if $pnoindels:
 --p-no-indels
#end if

--p-times=$ptimes

--p-overlap=$poverlap

#if $pmatchreadwildcards:
 --p-match-read-wildcards
#end if

#if $pnomatchadapterwildcards:
 --p-no-match-adapter-wildcards
#end if

--p-minimum-length=$pminimumlength

#if $pdiscarduntrimmed:
 --p-discard-untrimmed
#end if

--o-trimmed-sequences=otrimmedsequences

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp otrimmedsequences.qza $otrimmedsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed.     [required]" name="idemultiplexedsequences" optional="False" type="data" />
    <param label="--p-adapter: --p-adapter: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]           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. 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="padapter" selected="False" type="boolean" />
    <param label="--p-front: TEXT...     Sequence of an adapter ligated to the 5\' end. The List[Str]           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.                  [optional]" name="pfront" optional="False" type="text" />
    <param label="--p-anywhere: TEXT...  Sequence of an adapter that may be ligated to the 5\' List[Str]           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.                                 [optional]" name="panywhere" optional="False" type="text" />
    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.             [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
    <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                              [default: True]" name="pnoindels" selected="False" type="boolean" />
    <param label="--p-times: INTEGER     Remove multiple occurrences of an adapter if it is Range(1, None)      repeated, up to `times` times.            [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
    <param label="--p-overlap: INTEGER   Require at least `overlap` bases of overlap between Range(1, None)      read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
    <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
    <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
    <param label="--p-minimum-length: INTEGER Range(1, None)      Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
    <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
    
  </outputs>

  <help><![CDATA[
Find and remove adapters in demultiplexed single-end sequences.
###############################################################

Search demultiplexed single-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[SequencesWithQuality]
    The single-end sequences to be trimmed.
cores : Int % Range(1, None), optional
    Number of CPU cores to use.
adapter : 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. 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 : 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.
anywhere : 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.
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.
minimum_length : Int % Range(1, None), optional
    Discard reads shorter than specified value. Note, the cutadapt default
    of 0 has been overridden, because that value produces empty sequence
    records.
discard_untrimmed : Bool, optional
    Discard reads in which no adapter was found.

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