diff qiime2/qiime_quality-filter_q-score-joined.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-filter_q-score-joined.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,81 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-filter_q-score-joined" name="qiime quality-filter q-score-joined" version="2019.4">
+	<description> - Quality filter based on joined sequence quality scores.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime quality-filter q-score-joined
+
+--i-demux=$idemux
+
+#if $pminquality:
+ --p-min-quality=$pminquality
+#end if
+
+#if $pqualitywindow:
+ --p-quality-window=$pqualitywindow
+#end if
+
+#if $pminlengthfraction:
+ --p-min-length-fraction=$pminlengthfraction
+#end if
+
+#if $pmaxambiguous:
+ --p-max-ambiguous=$pmaxambiguous
+#end if
+
+--o-filtered-sequences=ofilteredsequences
+--o-filter-stats=ofilterstats
+;
+cp ofilteredsequences.qza $ofilteredsequences;
+cp ofilterstats.qza $ofilterstats
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[JoinedSequencesWithQuality] The demultiplexed sequence data to be quality filtered.                                    [required]" name="idemux" optional="False" type="data"/>
+		<param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores.                                    [default: 4]" name="pminquality" optional="True" type="integer" value="4"/>
+		<param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read.                             [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3"/>
+		<param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length.                                 [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75"/>
+		<param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`.                     [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences"/>
+		<data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats"/>
+	</outputs>
+	<help><![CDATA[
+Quality filter based on joined sequence quality scores.
+#######################################################
+
+This method filters joined sequence based on quality scores and the
+presence of ambiguous base calls.
+
+Parameters
+----------
+demux : SampleData[JoinedSequencesWithQuality]
+    The demultiplexed sequence data to be quality filtered.
+min_quality : Int, optional
+    The minimum acceptable PHRED score. All PHRED scores less that this
+    value are considered to be low PHRED scores.
+quality_window : Int, optional
+    The maximum number of low PHRED scores that can be observed in direct
+    succession before truncating a sequence read.
+min_length_fraction : Float, optional
+    The minimum length that a sequence read can be following truncation and
+    still be retained. This length should be provided as a fraction of the
+    input sequence length.
+max_ambiguous : Int, optional
+    The maximum number of ambiguous (i.e., N) base calls. This is applied
+    after trimming sequences based on `min_length_fraction`.
+
+Returns
+-------
+filtered_sequences : SampleData[JoinedSequencesWithQuality]
+    The resulting quality-filtered sequences.
+filter_stats : QualityFilterStats
+    Summary statistics of the filtering process.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>