diff qiime2/qiime_demux_emp-single.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_demux_emp-single.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,93 @@
+<?xml version="1.0" ?>
+<tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.4">
+	<description> - Demultiplex sequence data generated with the EMP protocol.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime demux emp-single
+
+--i-seqs=$iseqs
+--m-barcodes-column="$mbarcodescolumn"
+
+
+#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 + ',' + d['additional_input'].__getattr__('file_name')
+#end for
+#return $file_list
+#end def
+
+--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+
+
+#if $pnogolayerrorcorrection:
+ --p-no-golay-error-correction
+#end if
+
+#if $prevcompbarcodes:
+ --p-rev-comp-barcodes
+#end if
+
+#if $prevcompmappingbarcodes:
+ --p-rev-comp-mapping-barcodes
+#end if
+
+--o-per-sample-sequences=opersamplesequences
+--o-error-correction-details=oerrorcorrectiondetails
+;
+cp opersamplesequences.qza $opersamplesequences;
+cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
+	]]></command>
+	<inputs>
+		<repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
+			<param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
+		</repeat>
+
+		<param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
+		<param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes.                                    [required]" name="mbarcodescolumn" optional="False" type="text"/>
+		<param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads.                                  [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>
+		<param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/>
+		<param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing.                        [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${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[
+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
+protocol. Details about this protocol can be found at
+http://www.earthmicrobiome.org/protocols-and-standards/
+
+Parameters
+----------
+seqs : RawSequences | EMPSingleEndSequences | EMPPairedEndSequences
+    The single-end sequences to be demultiplexed.
+barcodes : MetadataColumn[Categorical]
+    The sample metadata column containing the per-sample barcodes.
+golay_error_correction : Bool, optional
+    Perform 12nt Golay error correction on the barcode reads.
+rev_comp_barcodes : Bool, optional
+    If provided, the barcode sequence reads will be reverse complemented
+    prior to demultiplexing.
+rev_comp_mapping_barcodes : Bool, optional
+    If provided, the barcode sequences in the sample metadata will be
+    reverse complemented prior to demultiplexing.
+
+Returns
+-------
+per_sample_sequences : SampleData[SequencesWithQuality]
+    The resulting demultiplexed sequences.
+error_correction_details : ErrorCorrectionDetails
+    Detail about the barcode error corrections.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>