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+++ b/qiime2/qiime_deblur_denoise-other.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,132 @@
+<?xml version="1.0" ?>
+<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other"
+      version="2020.8">
+  <description>Deblur sequences using a user-specified positive filter.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime deblur denoise-other
+
+--i-demultiplexed-seqs=$idemultiplexedseqs
+
+--i-reference-seqs=$ireferenceseqs
+
+--p-trim-length=$ptrimlength
+
+--p-left-trim-len=$plefttrimlen
+
+#if $psamplestats:
+ --p-sample-stats
+#end if
+
+--p-mean-error=$pmeanerror
+
+--p-indel-prob=$pindelprob
+
+--p-indel-max=$pindelmax
+
+--p-min-reads=$pminreads
+
+--p-min-size=$pminsize
+
+--p-jobs-to-start=$pjobstostart
+
+#if $pnohashedfeatureids:
+ --p-no-hashed-feature-ids
+#end if
+
+--o-table=otable
+
+--o-representative-sequences=orepresentativesequences
+
+--o-stats=ostats
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ostats.qza $ostats
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences.               [required]" name="ireferenceseqs" optional="False" type="data" />
+    <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming.                                  [required]" name="ptrimlength" optional="False" type="text" />
+    <param label="--p-left-trim-len: INTEGER Range(0, None)       Sequence trimming from the 5\' end. A value of 0 will disable this trim.                       [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
+    <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample.    [default: False]" name="psamplestats" selected="False" type="boolean" />
+    <param label="--p-mean-error: NUMBER  The mean per nucleotide error, used for original sequence estimate.                   [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005" />
+    <param label="--p-indel-prob: NUMBER  Insertion/deletion (indel) probability (same for N indels).                              [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01" />
+    <param label="--p-indel-max: INTEGER  Maximum number of insertion/deletions.   [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
+    <param label="--p-min-reads: INTEGER  Retain only features appearing at least min-reads times across all samples in the resulting feature table.                                  [default: 10]" name="pminreads" optional="True" type="integer" value="10" />
+    <param label="--p-min-size: INTEGER   In each sample, discard all features with an abundance less than min-size.            [default: 2]" name="pminsize" optional="True" type="integer" value="2" />
+    <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs.        [default: True]" name="pnohashedfeatureids" 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 ${on_string}: table.qza" name="otable" />
+    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
+    <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Deblur sequences using a user-specified positive filter.
+###############################################################
+
+Perform sequence quality control for Illumina data using the Deblur
+workflow, including positive alignment-based filtering. Only forward reads
+are supported at this time. This mode of execution is particularly useful
+when operating on non-16S data. For example, to apply Deblur to 18S data,
+you would want to specify a reference composed of 18S sequences in order to
+filter out sequences which do not appear to be 18S. The assessment is
+performed by local alignment using SortMeRNA with a permissive e-value
+threshold.
+
+Parameters
+----------
+demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
+    The demultiplexed sequences to be denoised.
+reference_seqs : FeatureData[Sequence]
+    Positive filtering database. Keep all sequences aligning to these
+    sequences.
+trim_length : Int
+    Sequence trim length, specify -1 to disable trimming.
+left_trim_len : Int % Range(0, None), optional
+    Sequence trimming from the 5' end. A value of 0 will disable this trim.
+sample_stats : Bool, optional
+    If true, gather stats per sample.
+mean_error : Float, optional
+    The mean per nucleotide error, used for original sequence estimate.
+indel_prob : Float, optional
+    Insertion/deletion (indel) probability (same for N indels).
+indel_max : Int, optional
+    Maximum number of insertion/deletions.
+min_reads : Int, optional
+    Retain only features appearing at least min_reads times across all
+    samples in the resulting feature table.
+min_size : Int, optional
+    In each sample, discard all features with an abundance less than
+    min_size.
+jobs_to_start : Int, optional
+    Number of jobs to start (if to run in parallel).
+hashed_feature_ids : Bool, optional
+    If true, hash the feature IDs.
+
+Returns
+-------
+table : FeatureTable[Frequency]
+    The resulting denoised feature table.
+representative_sequences : FeatureData[Sequence]
+    The resulting feature sequences.
+stats : DeblurStats
+    Per-sample stats if requested.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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