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diff qiime2/qiime_vsearch_join-pairs.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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line diff
--- a/qiime2/qiime_vsearch_join-pairs.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_vsearch_join-pairs.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,92 +1,87 @@
 <?xml version="1.0" ?>
-<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2019.7">
-	<description> - Join paired-end reads.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs"
+      version="2020.8">
+  <description>Join paired-end reads.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime vsearch join-pairs
 
 --i-demultiplexed-seqs=$idemultiplexedseqs
 
 #if str($ptruncqual):
- --p-truncqual="$ptruncqual"
+  --p-truncqual=$ptruncqual
 #end if
-
-#if str($pminlen):
- --p-minlen=$pminlen
-#end if
+--p-minlen=$pminlen
 
 #if str($pmaxns):
- --p-maxns="$pmaxns"
+  --p-maxns=$pmaxns
 #end if
-
 #if $pallowmergestagger:
  --p-allowmergestagger
 #end if
 
-#if str($pminovlen):
- --p-minovlen=$pminovlen
-#end if
+--p-minovlen=$pminovlen
 
-#if str($pmaxdiffs):
- --p-maxdiffs=$pmaxdiffs
-#end if
+--p-maxdiffs=$pmaxdiffs
 
 #if str($pminmergelen):
- --p-minmergelen="$pminmergelen"
+  --p-minmergelen=$pminmergelen
 #end if
-
 #if str($pmaxmergelen):
- --p-maxmergelen="$pmaxmergelen"
+  --p-maxmergelen=$pmaxmergelen
 #end if
-
 #if str($pmaxee):
- --p-maxee="$pmaxee"
+  --p-maxee=$pmaxee
 #end if
+--p-qmin=$pqmin
+
+--p-qminout=$pqminout
+
+--p-qmax=$pqmax
 
-#if str($pqmin):
- --p-qmin=$pqmin
-#end if
+--p-qmaxout=$pqmaxout
+
+--p-threads=$pthreads
 
-#if str($pqminout):
- --p-qminout=$pqminout
+--o-joined-sequences=ojoinedsequences
+
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
-#if str($pqmax):
- --p-qmax=$pqmax
-#end if
-
-#if str($pqmaxout):
- --p-qmaxout=$pqmaxout
-#end if
-
---o-joined-sequences=ojoinedsequences
 ;
 cp ojoinedsequences.qza $ojoinedsequences
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
-		<param label="--p-truncqual: INTEGER  Truncate sequences at the first base with the Range(0, None)       specified quality score value or lower.    [optional]" name="ptruncqual" optional="True" min="0" type="integer"/>
-		<param label="--p-minlen: INTEGER     Sequences shorter than minlen after truncation are Range(0, None)       discarded.                               [default: 1]" name="pminlen" optional="True" type="integer" min="0" value="1"/>
-		<param label="--p-maxns: INTEGER      Sequences with more than maxns N characters are Range(0, None)       discarded.                                 [optional]" name="pmaxns" optional="True" min="0" type="integer"/>
-		<param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean"/>
-		<param label="--p-minovlen: INTEGER   Minimum overlap length of forward and reverse reads Range(0, None)       for joining.                            [default: 10]" name="pminovlen" optional="True" type="integer" min="0" value="10"/>
-		<param label="--p-maxdiffs: INTEGER   Maximum number of mismatches in the forward/reverse Range(0, None)       read overlap for joining.               [default: 10]" name="pmaxdiffs" optional="True" type="integer" min="0" value="10"/>
-		<param label="--p-minmergelen: INTEGER Range(0, None)       Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="True" min="0" type="integer"/>
-		<param label="--p-maxmergelen: INTEGER Range(0, None)       Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="True" min="0" type="integer"/>
-		<param label="--p-maxee: NUMBER       Maximum number of expected errors in the joined read Range(0.0, None)     to be retained.                            [optional]" name="pmaxee" optional="True" min="0" type="float"/>
-		<param label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" name="pqmin" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
-		<param label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" name="pqminout" optional="True" type="integer" min="-5" max="2" exclude_max="False" value="0"/>
-		<param label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" name="pqmax" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
-		<param label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" name="pqmaxout" optional="True" type="integer" min="40" max="41" exclude_max="False" value="41"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: joinedsequences.qza" name="ojoinedsequences"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data" />
+    <param label="--p-truncqual: INTEGER  Truncate sequences at the first base with the Range(0, None)       specified quality score value or lower.    [optional]" name="ptruncqual" optional="False" type="text" />
+    <param label="--p-minlen: INTEGER     Sequences shorter than minlen after truncation are Range(0, None)       discarded.                               [default: 1]" min="0" name="pminlen" optional="True" type="integer" value="1" />
+    <param label="--p-maxns: INTEGER      Sequences with more than maxns N characters are Range(0, None)       discarded.                                 [optional]" name="pmaxns" optional="False" type="text" />
+    <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" />
+    <param label="--p-minovlen: INTEGER   Minimum overlap length of forward and reverse reads Range(0, None)       for joining.                            [default: 10]" min="0" name="pminovlen" optional="True" type="integer" value="10" />
+    <param label="--p-maxdiffs: INTEGER   Maximum number of mismatches in the forward/reverse Range(0, None)       read overlap for joining.               [default: 10]" min="0" name="pmaxdiffs" optional="True" type="integer" value="10" />
+    <param label="--p-minmergelen: INTEGER Range(0, None)       Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="False" type="text" />
+    <param label="--p-maxmergelen: INTEGER Range(0, None)       Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="False" type="text" />
+    <param label="--p-maxee: NUMBER       Maximum number of expected errors in the joined read Range(0.0, None)     to be retained.                            [optional]" name="pmaxee" optional="False" type="text" />
+    <param exclude_max="False" label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" max="2" min="-5" name="pqmin" optional="True" type="integer" value="0" />
+    <param exclude_max="False" label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" max="2" min="-5" name="pqminout" optional="True" type="integer" value="0" />
+    <param exclude_max="False" label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" max="41" min="40" name="pqmax" optional="True" type="integer" value="41" />
+    <param exclude_max="False" label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" max="41" min="40" name="pqmaxout" optional="True" type="integer" value="41" />
+    <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}: joinedsequences.qza" name="ojoinedsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Join paired-end reads.
-######################
+###############################################################
 
 Join paired-end sequence reads using vsearch's merge_pairs function. The
 qmin, qminout, qmax, and qmaxout parameters should only need to be modified
@@ -126,14 +121,17 @@
     The maximum allowed quality score in the input.
 qmaxout : Int % Range(40, 41, inclusive_end=True), optional
     The maximum allowed quality score to use in output.
+threads : Int % Range(0, 8, inclusive_end=True), optional
+    The number of threads to use for computation. Does not scale much past
+    4 threads.
 
 Returns
 -------
 joined_sequences : SampleData[JoinedSequencesWithQuality]
     The joined sequences.
-	]]></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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