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diff qiime2/qiime_vsearch_uchime-ref.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_vsearch_uchime-ref.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_uchime-ref.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,67 +1,68 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2019.7">
-	<description> - Reference-based chimera filtering with vsearch.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref"
+      version="2020.8">
+  <description>Reference-based chimera filtering with vsearch.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime vsearch uchime-ref
 
 --i-sequences=$isequences
+
 --i-table=$itable
+
 --i-reference-sequences=$ireferencesequences
 
-#if str($pdn):
- --p-dn=$pdn
-#end if
+--p-dn=$pdn
+
+--p-mindiffs=$pmindiffs
 
-#if str($pmindiffs):
- --p-mindiffs=$pmindiffs
-#end if
+--p-mindiv=$pmindiv
+
+--p-minh=$pminh
+
+--p-xn=$pxn
 
-#if str($pmindiv):
- --p-mindiv=$pmindiv
-#end if
+--p-threads=$pthreads
+
+--o-chimeras=ochimeras
 
-#if str($pminh):
- --p-minh=$pminh
-#end if
+--o-nonchimeras=ononchimeras
 
-#if str($pxn):
- --p-xn=$pxn
+--o-stats=ostats
+
+#if str($examples) != 'None':
+--examples=$examples
 #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[
+
+  ]]></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]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
+    <param label="--p-mindiffs: INTEGER    Minimum number of differences per segment. Range(1, None)                                                [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
+    <param label="--p-mindiv: NUMBER       Minimum divergence from closest parent. Range(0.0, None)                                            [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
+    <param exclude_max="False" 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]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
+    <param exclude_min="True" 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]" max="None" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
+    <data format="qza" label="${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
@@ -101,9 +102,9 @@
     The non-chimeric sequences.
 stats : UchimeStats
     Summary statistics from chimera checking.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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