Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_cutadapt_trim-single.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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--- a/qiime2/qiime_cutadapt_trim-single.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_cutadapt_trim-single.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,77 +1,58 @@
 <?xml version="1.0" ?>
-<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2019.7">
-	<description> - Find and remove adapters in demultiplexed single-end sequences.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
+      version="2020.8">
+  <description>Find and remove adapters in demultiplexed single-end sequences.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime cutadapt trim-single
+
 --i-demultiplexed-sequences=$idemultiplexedsequences
 
-#set $pcores = '${GALAXY_SLOTS:-4}'
-#if str($pcores):
 --p-cores=$pcores
-#end if
-
-
-#if '__sq__' in str($padapter):
-  #set $padapter_temp = $padapter.replace('__sq__', "'")
-  #set $padapter = $padapter_temp
-#end if
 
-#if 'X' in str($padapter):
-  #set $padapter_temp = $padapter.replace('X', "$")
-  #set $padapter = $padapter_temp
-#end if
-
-#if str($padapter):
- --p-adapter="$padapter"
-#end if
-
-
-
-
-
-#if '__sq__' in str($pfront):
-  #set $pfront_temp = $pfront.replace('__sq__', "'")
-  #set $pfront = $pfront_temp
+#if $padapter:
+ --p-adapter
 #end if
 
 #if str($pfront):
- --p-front="$pfront"
+  --p-front=$pfront
+#end if
+#if '__ob__' in str($panywhere):
+  #set $panywhere_temp = $panywhere.replace('__ob__', '[')
+  #set $panywhere = $panywhere_temp
 #end if
-
-
-
-
-
+#if '__cb__' in str($panywhere):
+  #set $panywhere_temp = $panywhere.replace('__cb__', ']')
+  #set $panywhere = $panywhere_temp
+#end if
+#if 'X' in str($panywhere):
+  #set $panywhere_temp = $panywhere.replace('X', '\\')
+  #set $panywhere = $panywhere_temp
+#end if
 #if '__sq__' in str($panywhere):
   #set $panywhere_temp = $panywhere.replace('__sq__', "'")
   #set $panywhere = $panywhere_temp
 #end if
-
-#if str($panywhere):
- --p-anywhere="$panywhere"
+#if '__db__' in str($panywhere):
+  #set $panywhere_temp = $panywhere.replace('__db__', '"')
+  #set $panywhere = $panywhere_temp
 #end if
 
-
-
+#if str($panywhere):
+  --p-anywhere=$panywhere
+#end if
 
-#if str($perrorrate):
- --p-error-rate=$perrorrate
-#end if
+--p-error-rate=$perrorrate
 
 #if $pnoindels:
  --p-no-indels
 #end if
 
-#if str($ptimes):
- --p-times=$ptimes
-#end if
+--p-times=$ptimes
 
-#if str($poverlap):
- --p-overlap=$poverlap
-#end if
+--p-overlap=$poverlap
 
 #if $pmatchreadwildcards:
  --p-match-read-wildcards
@@ -81,9 +62,7 @@
  --p-no-match-adapter-wildcards
 #end if
 
-#if str($pminimumlength):
- --p-minimum-length=$pminimumlength
-#end if
+--p-minimum-length=$pminimumlength
 
 #if $pdiscarduntrimmed:
  --p-discard-untrimmed
@@ -91,28 +70,37 @@
 
 --o-trimmed-sequences=otrimmedsequences
 
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp otrimmedsequences.qza $otrimmedsequences
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed.     [required]" name="idemultiplexedsequences" optional="False" type="data"/>
-		<param label="--p-adapter: TEXT...   Sequence of an adapter ligated to the 3' end. The List[Str]           adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. If your sequence of interest is 'framed' by a 5' and a 3' adapter, use this parameter to define a 'linked' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapter" optional="True" type="text"/>
-		<param label="--p-front: TEXT...     Sequence of an adapter ligated to the 5' end. The List[Str]           adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read.                  [optional]" name="pfront" optional="True" type="text"/>
-		<param label="--p-anywhere: TEXT...  Sequence of an adapter that may be ligated to the 5' List[Str]           or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to.                                 [optional]" name="panywhere" optional="True" type="text"/>
 
-		<param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.             [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
-		<param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                              [default: False]" name="pnoindels" selected="False" type="boolean"/>
-		<param label="--p-times: INTEGER     Remove multiple occurrences of an adapter if it is Range(1, None)      repeated, up to `times` times.            [default: 1]" name="ptimes" optional="True" type="integer" min="1" value="1"/>
-		<param label="--p-overlap: INTEGER   Require at least `overlap` bases of overlap between Range(1, None)      read and adapter for an adapter to be found. [default: 3]" name="poverlap" optional="True" type="integer" min="1" value="3"/>
-		<param label="--p-match-read-wildcards: --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean"/>
-		<param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: False]" name="pnomatchadapterwildcards" selected="False" type="boolean"/>
-		<param label="--p-minimum-length: INTEGER Range(1, None)      Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" name="pminimumlength" optional="True" type="integer" min="1" value="1"/>
-		<param label="--p-discard-untrimmed: --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed.     [required]" name="idemultiplexedsequences" optional="False" type="data" />
+    <param label="--p-adapter: --p-adapter: TEXT...   Sequence of an adapter ligated to the 3\' end. The List[Str]           adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapter" selected="False" type="boolean" />
+    <param label="--p-front: TEXT...     Sequence of an adapter ligated to the 5\' end. The List[Str]           adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read.                  [optional]" name="pfront" optional="False" type="text" />
+    <param label="--p-anywhere: TEXT...  Sequence of an adapter that may be ligated to the 5\' List[Str]           or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to.                                 [optional]" name="panywhere" optional="False" type="text" />
+    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate.             [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
+    <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters.                              [default: True]" name="pnoindels" selected="False" type="boolean" />
+    <param label="--p-times: INTEGER     Remove multiple occurrences of an adapter if it is Range(1, None)      repeated, up to `times` times.            [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
+    <param label="--p-overlap: INTEGER   Require at least `overlap` bases of overlap between Range(1, None)      read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
+    <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
+    <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
+    <param label="--p-minimum-length: INTEGER Range(1, None)      Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
+    <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" 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}: trimmedsequences.qza" name="otrimmedsequences" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Find and remove adapters in demultiplexed single-end sequences.
 ###############################################################
 
@@ -125,6 +113,8 @@
 ----------
 demultiplexed_sequences : SampleData[SequencesWithQuality]
     The single-end sequences to be trimmed.
+cores : Int % Range(1, None), optional
+    Number of CPU cores to use.
 adapter : List[Str], optional
     Sequence of an adapter ligated to the 3' end. The adapter and any
     subsequent bases are trimmed. If a `$` is appended, the adapter is only
@@ -169,9 +159,9 @@
 -------
 trimmed_sequences : SampleData[SequencesWithQuality]
     The resulting trimmed sequences.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file