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diff qiime2/qiime_deblur_denoise-other.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_deblur_denoise-other.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_deblur_denoise-other.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,87 +1,81 @@
 <?xml version="1.0" ?>
-<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2019.7">
-	<description> - Deblur sequences using a user-specified positive filter.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<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
 
-#if str($ptrimlength):
- --p-trim-length="$ptrimlength"
-#end if
+--p-trim-length=$ptrimlength
 
-#if str($plefttrimlen):
- --p-left-trim-len=$plefttrimlen
-#end if
+--p-left-trim-len=$plefttrimlen
 
-#if str($psamplestats):
+#if $psamplestats:
  --p-sample-stats
 #end if
 
-#if str($pmeanerror):
- --p-mean-error=$pmeanerror
-#end if
+--p-mean-error=$pmeanerror
 
-#if str($pindelprob):
- --p-indel-prob=$pindelprob
-#end if
+--p-indel-prob=$pindelprob
 
-#if str($pindelmax):
- --p-indel-max=$pindelmax
-#end if
+--p-indel-max=$pindelmax
 
-#if str($pminreads):
- --p-min-reads=$pminreads
-#end if
+--p-min-reads=$pminreads
 
-#if str($pminsize):
- --p-min-size=$pminsize
-#end if
+--p-min-size=$pminsize
 
-#set $pjobstostart = '${GALAXY_SLOTS:-4}'
+--p-jobs-to-start=$pjobstostart
 
-#if str($pjobstostart):
- --p-jobs-to-start="$pjobstostart"
-#end if
-
-
-#if str($pnohashedfeatureids):
+#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 otable.qza $otable;
-cp orepresentativesequences.qza $orepresentativesequences;
 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" value="" type="integer"/>
-		<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]" name="plefttrimlen" optional="True" type="integer" min="0" value="0"/>
-		<param label="--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: If false, hash the feature IDs.        [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
-	</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[
+
+  ]]></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
@@ -117,6 +111,8 @@
 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.
 
@@ -128,9 +124,9 @@
     The resulting feature sequences.
 stats : DeblurStats
     Per-sample stats if requested.
-	]]></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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