--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_trim-paired.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,190 @@
+<?xml version="1.0" ?>
+<tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2019.4">
+	<description> - Find and remove adapters in demultiplexed paired-end sequences.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime cutadapt trim-paired
+
+--i-demultiplexed-sequences=$idemultiplexedsequences
+
+#set $pcores = '${GALAXY_SLOTS:-4}'
+#if str($pcores):
+--p-cores=$pcores
+#end if
+
+#if str($padapterf):
+ --p-adapter-f="$padapterf"
+#end if
+
+#if str($pfrontf):
+ --p-front-f="$pfrontf"
+#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="$panywheref"
+#end if
+
+
+#if str($padapterr):
+ --p-adapter-r="$padapterr"
+#end if
+
+#if str($pfrontr):
+ --p-front-r="$pfrontr"
+#end if
+
+#if '__sq__' in str($panywherer):
+  #set $panywherer_temp = $panywherer.replace('__sq__', "'")
+  #set $panywherer = $panywherer_temp
+#end if
+
+#if str($panywherer):
+ --p-anywhere-r="$panywherer"
+#end if
+
+#if $perrorrate:
+ --p-error-rate=$perrorrate
+#end if
+
+#if $pnoindels:
+ --p-no-indels
+#end if
+
+#if $ptimes:
+ --p-times=$ptimes
+#end if
+
+#if $poverlap:
+ --p-overlap=$poverlap
+#end if
+
+#if $pmatchreadwildcards:
+ --p-match-read-wildcards
+#end if
+
+#if $pnomatchadapterwildcards:
+ --p-no-match-adapter-wildcards
+#end if
+
+#if $pminimumlength:
+ --p-minimum-length=$pminimumlength
+#end if
+
+#if $pdiscarduntrimmed:
+ --p-discard-untrimmed
+#end if
+
+--o-trimmed-sequences=otrimmedsequences
+;
+
+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="True" type="text"/>
+		<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="True" 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="True" 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="True" type="text"/>
+		<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="True" 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="True" type="text"/>
+		<param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.           [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
+		<param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                   [default: False]" 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]" name="ptimes" optional="True" type="integer" min="1" 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]" name="poverlap" optional="True" type="integer" min="1" 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" selected="False" type="boolean"/>
+		<param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: False]" 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]" name="pminimumlength" optional="True" type="integer" min="1" value="1"/>
+		<param label="--p-discard-untrimmed: --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
+	</outputs>
+	<help><![CDATA[
+Find and remove adapters in demultiplexed paired-end sequences.
+###############################################################
+
+Search demultiplexed paired-end sequences for adapters and remove them. The
+parameter descriptions in this method are adapted from the official
+cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
+for complete details.
+
+Parameters
+----------
+demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
+    The paired-end sequences to be trimmed.
+adapter_f : List[Str], optional
+    Sequence of an adapter ligated to the 3' end. The adapter and any
+    subsequent bases are trimmed. If a `$` 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>