Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_demux_emp-single.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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line diff
--- a/qiime2/qiime_demux_emp-single.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_demux_emp-single.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,26 +1,47 @@
 <?xml version="1.0" ?>
-<tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.7">
-	<description> - Demultiplex sequence data generated with the EMP protocol.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_demux_emp-single" name="qiime demux emp-single"
+      version="2020.8">
+  <description>Demultiplex sequence data generated with the EMP protocol.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime demux emp-single
 
 --i-seqs=$iseqs
---m-barcodes-column="$mbarcodescolumn"
-
+# if $input_files_mbarcodesfile:
+  # def list_dict_to_string(list_dict):
+    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+    # for d in list_dict[1:]:
+      # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+# end if
 
-#if $input_files_mbarcodesfile:
-#def list_dict_to_string(list_dict):
-#set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
-#for d in list_dict[1:]:
-	#set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+#if '__ob__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__cb__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
 #end if
+#if 'X' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__sq__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if '__db__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+
+--m-barcodes-column=$mbarcodescolumn
 
 
 #if $pnogolayerrorcorrection:
@@ -36,29 +57,39 @@
 #end if
 
 --o-per-sample-sequences=opersamplesequences
+
 --o-error-correction-details=oerrorcorrectiondetails
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp opersamplesequences.qza $opersamplesequences;
 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
-	]]></command>
-	<inputs>
-		<repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]">
-			<param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
-		</repeat>
 
-		<param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
-		<param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text"/>
-		<param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>
-		<param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/>
-		<param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
-		<data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
+    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text" />
+    <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
+    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
+    <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
+    <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Demultiplex sequence data generated with the EMP protocol.
-##########################################################
+###############################################################
 
 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
 generated with the Earth Microbiome Project (EMP) amplicon sequencing
@@ -86,9 +117,9 @@
     The resulting demultiplexed sequences.
 error_correction_details : ErrorCorrectionDetails
     Detail about the barcode error corrections.
-	]]></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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