diff qiime2/qiime_vsearch_uchime-ref.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_uchime-ref.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,109 @@
+<?xml version="1.0" ?>
+<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.4">
+	<description> - Reference-based chimera filtering with vsearch.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime vsearch uchime-ref
+
+--i-sequences=$isequences
+--i-table=$itable
+--i-reference-sequences=$ireferencesequences
+
+#if $pdn:
+ --p-dn=$pdn
+#end if
+
+#if $pmindiffs:
+ --p-mindiffs=$pmindiffs
+#end if
+
+#if $pmindiv:
+ --p-mindiv=$pmindiv
+#end if
+
+#if $pminh:
+ --p-minh=$pminh
+#end if
+
+#if $pxn:
+ --p-xn=$pxn
+#end if
+
+#set $pthreads = '${GALAXY_SLOTS:-4}'
+#if str($pthreads):
+ --p-threads="$pthreads"
+#end if
+
+--o-chimeras=ochimeras
+--o-nonchimeras=ononchimeras
+--o-stats=ostats
+;
+cp ochimeras.qza $ochimeras;
+cp ononchimeras.qza $ononchimeras;
+cp ostats.qza $ostats
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances).                              [required]" name="itable" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences.     [required]" name="ireferencesequences" optional="False" type="data"/>
+		<param label="--p-dn: NUMBER           No vote pseudo-count, corresponding to the Range(0.0, None)      parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
+		<param label="--p-mindiffs: INTEGER    Minimum number of differences per segment. Range(1, None)                                                [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
+		<param label="--p-mindiv: NUMBER       Minimum divergence from closest parent. Range(0.0, None)                                            [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
+		<param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity.                         [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
+		<param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function.              [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_min="True" value="8.0"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
+		<data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
+		<data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
+	</outputs>
+	<help><![CDATA[
+Reference-based chimera filtering with vsearch.
+###############################################
+
+Apply the vsearch uchime_ref method to identify chimeric feature sequences.
+The results of this method can be used to filter chimeric features from the
+corresponding feature table. For additional details, please refer to the
+vsearch documentation.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The feature sequences to be chimera-checked.
+table : FeatureTable[Frequency]
+    Feature table (used for computing total feature abundances).
+reference_sequences : FeatureData[Sequence]
+    The non-chimeric reference sequences.
+dn : Float % Range(0.0, None), optional
+    No vote pseudo-count, corresponding to the parameter n in the chimera
+    scoring function.
+mindiffs : Int % Range(1, None), optional
+    Minimum number of differences per segment.
+mindiv : Float % Range(0.0, None), optional
+    Minimum divergence from closest parent.
+minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
+    Minimum score (h). Increasing this value tends to reduce the number of
+    false positives and to decrease sensitivity.
+xn : Float % Range(1.0, None, inclusive_start=False), optional
+    No vote weight, corresponding to the parameter beta in the scoring
+    function.
+threads : Int % Range(0, 256, inclusive_end=True), optional
+    The number of threads to use for computation. Passing 0 will launch one
+    thread per CPU core.
+
+Returns
+-------
+chimeras : FeatureData[Sequence]
+    The chimeric sequences.
+nonchimeras : FeatureData[Sequence]
+    The non-chimeric sequences.
+stats : UchimeStats
+    Summary statistics from chimera checking.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>