--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-paired.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,219 @@
+<?xml version="1.0" ?>
+<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired"
+      version="2020.8">
+  <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime cutadapt trim-paired
+
+--i-demultiplexed-sequences=$idemultiplexedsequences
+
+--p-cores=$pcores
+
+#if str($padapterf):
+  --p-adapter-f=$padapterf
+#end if
+#if str($pfrontf):
+  --p-front-f=$pfrontf
+#end if
+#if '__ob__' in str($panywheref):
+  #set $panywheref_temp = $panywheref.replace('__ob__', '[')
+  #set $panywheref = $panywheref_temp
+#end if
+#if '__cb__' in str($panywheref):
+  #set $panywheref_temp = $panywheref.replace('__cb__', ']')
+  #set $panywheref = $panywheref_temp
+#end if
+#if 'X' in str($panywheref):
+  #set $panywheref_temp = $panywheref.replace('X', '\\')
+  #set $panywheref = $panywheref_temp
+#end if
+#if '__sq__' in str($panywheref):
+  #set $panywheref_temp = $panywheref.replace('__sq__', "'")
+  #set $panywheref = $panywheref_temp
+#end if
+#if '__db__' in str($panywheref):
+  #set $panywheref_temp = $panywheref.replace('__db__', '"')
+  #set $panywheref = $panywheref_temp
+#end if
+
+#if str($panywheref):
+  --p-anywhere-f=$panywheref
+#end if
+
+#if str($padapterr):
+  --p-adapter-r=$padapterr
+#end if
+#if str($pfrontr):
+  --p-front-r=$pfrontr
+#end if
+#if '__ob__' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('__ob__', '[')
+  #set $panywherer = $panywherer_temp
+#end if
+#if '__cb__' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('__cb__', ']')
+  #set $panywherer = $panywherer_temp
+#end if
+#if 'X' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('X', '\\')
+  #set $panywherer = $panywherer_temp
+#end if
+#if '__sq__' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('__sq__', "'")
+  #set $panywherer = $panywherer_temp
+#end if
+#if '__db__' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('__db__', '"')
+  #set $panywherer = $panywherer_temp
+#end if
+
+#if str($panywherer):
+  --p-anywhere-r=$panywherer
+#end if
+
+--p-error-rate=$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 $otrimmedsequences
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed.   [required]" name="idemultiplexedsequences" optional="False" type="data" />
+    <param label="--p-adapter-f: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]             adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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="False" type="text" value="False" />
+    <param label="--p-front-f: 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. Search in forward read.                             [optional]" name="pfrontf" optional="False" type="text" />
+    <param label="--p-anywhere-f: TEXT...  Sequence of an adapter that may be ligated to the List[Str]             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="False" type="text" />
+    <param label="--p-adapter-r: 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. 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="False" type="text" value="False" />
+    <param label="--p-front-r: 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. Search in reverse read.                             [optional]" name="pfrontr" optional="False" type="text" />
+    <param label="--p-anywhere-r: TEXT...  Sequence of an adapter that may be ligated to the List[Str]             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="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 ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Find and remove adapters in demultiplexed paired-end sequences.
+###############################################################
+
+Search demultiplexed paired-end sequences for adapters and remove them. The
+parameter descriptions in this method are adapted from the official
+cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
+for complete details.
+
+Parameters
+----------
+demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
+    The paired-end sequences to be trimmed.
+cores : Int % Range(1, None), optional
+    Number of CPU cores to use.
+adapter_f : List[Str], optional
+    Sequence of an adapter ligated to the 3' end. The adapter and any
+    subsequent bases are trimmed. If a `$` 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.
+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[PairedEndSequencesWithQuality]
+    The resulting trimmed sequences.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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