--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_quality-control_filter-reads.xml	Thu Sep 03 09:33:04 2020 +0000
@@ -0,0 +1,110 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-control_filter-reads" name="qiime quality-control filter-reads"
+      version="2020.8">
+  <description>Filter demultiplexed sequences by alignment to reference database.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime quality-control filter-reads
+
+--i-demultiplexed-sequences=$idemultiplexedsequences
+
+--i-database=$idatabase
+
+--p-n-threads=$pnthreads
+
+#if str($pmode) != 'None':
+--p-mode=$pmode
+#end if
+
+#if str($psensitivity) != 'None':
+--p-sensitivity=$psensitivity
+#end if
+
+--p-ref-gap-open-penalty=$prefgapopenpenalty
+
+--p-ref-gap-ext-penalty=$prefgapextpenalty
+
+#if $pnoexcludeseqs:
+ --p-no-exclude-seqs
+#end if
+
+--o-filtered-sequences=ofilteredsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofilteredsequences.qza $ofilteredsequences
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed.               [required]" name="idemultiplexedsequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-database: ARTIFACT  Bowtie2 indexed database. Bowtie2Index                                                    [required]" name="idatabase" optional="False" type="data" />
+    <param label="--p-mode: " name="pmode" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="local">local</option>
+      <option value="global">global</option>
+    </param>
+    <param label="--p-sensitivity: " name="psensitivity" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="very-fast">very-fast</option>
+      <option value="fast">fast</option>
+      <option value="sensitive">sensitive</option>
+      <option value="very-sensitive">very-sensitive</option>
+    </param>
+    <param label="--p-ref-gap-open-penalty: INTEGER Range(1, None)       Reference gap open penalty.              [default: 5]" min="1" name="prefgapopenpenalty" optional="True" type="integer" value="5" />
+    <param label="--p-ref-gap-ext-penalty: INTEGER Range(1, None)       Reference gap extend penalty.            [default: 3]" min="1" name="prefgapextpenalty" optional="True" type="integer" value="3" />
+    <param label="--p-no-exclude-seqs: Do not exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database.      [default: True]" name="pnoexcludeseqs" 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}: filteredsequences.qza" name="ofilteredsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Filter demultiplexed sequences by alignment to reference database.
+###############################################################
+
+Filter out (or keep) demultiplexed single- or paired-end sequences that
+align to a reference database, using bowtie2 and samtools. This method can
+be used to filter out human DNA sequences and other contaminants in any
+FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
+alternatively (when exclude_seqs is False) to only keep sequences that do
+align to the reference.
+
+Parameters
+----------
+demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
+    The sequences to be trimmed.
+database : Bowtie2Index
+    Bowtie2 indexed database.
+n_threads : Int % Range(1, None), optional
+    Number of alignment threads to launch.
+mode : Str % Choices('local', 'global'), optional
+    Bowtie2 alignment settings. See bowtie2 manual for more details.
+sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
+    Bowtie2 alignment sensitivity. See bowtie2 manual for details.
+ref_gap_open_penalty : Int % Range(1, None), optional
+    Reference gap open penalty.
+ref_gap_ext_penalty : Int % Range(1, None), optional
+    Reference gap extend penalty.
+exclude_seqs : Bool, optional
+    Exclude sequences that align to reference. Set this option to False to
+    exclude sequences that do not align to the reference database.
+
+Returns
+-------
+filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
+    The resulting filtered sequences.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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