Mercurial > repos > florianbegusch > qiime2_suite

changeset 16:5021f9d76de4 draft

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Deleted selected files
author florianbegusch
date Thu, 03 Sep 2020 10:51:34 +0000
parents 276ec629f09a
children 424d74a76037
files qiime2/qiime_tools_export.xml qiime2/qiime_tools_export_collection.xml qiime2/qiime_tools_export_paired_collection.xml qiime2/qiime_tools_import.xml
diffstat 4 files changed, 0 insertions(+), 365 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2/qiime_tools_export.xml	Thu Sep 03 09:56:05 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_tools_export" name="qiime tools export --input-path" version="2019.7">
-	<description> - Export data from a QIIME 2 Artifact or Visualization.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[qiime tools export --input-path $isequences --output-path test
-	]]></command>
-	<inputs>
-	<param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data"/></inputs>
-	
-	<outputs>
-    <data format="txt" name="report">
-        <discover_datasets pattern="__designation_and_ext__" directory="test" visible="true" />
-    </data>
-	</outputs>
-	
-	<!--<outputs>
-	
-   <collection type="list" label="Exported artifact" name="output1">
-     <discover_datasets pattern="*.*" directory="test" />
-   </collection>
- </outputs>-->
-	<help>
-</help>
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
--- a/qiime2/qiime_tools_export_collection.xml	Thu Sep 03 09:56:05 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="qiime_tools_export_collection" name="qiime tools export --input-path collection" version="2019.7">
-   <description>- Export data from a QIIME 2 Artifact or Visualization.</description>
-   <requirements>
-      <requirement type="package" version="2019.7">qiime2</requirement>
-   </requirements>
-   <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command>
-   <inputs>
-      <param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data" />
-   </inputs>
-
-   <outputs>
-      <collection type="list" label="Export artifact to collection" name="output">
-         <discover_datasets pattern="__designation_and_ext__" directory="test" />
-      </collection>
-   </outputs>
-   <help />
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
\ No newline at end of file
--- a/qiime2/qiime_tools_export_paired_collection.xml	Thu Sep 03 09:56:05 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<tool id="qiime_tools_export_paired_collection" name="qiime tools export --input-path to paired collection" version="2019.7">
-   <description>- Export data from a QIIME 2 Artifact or Visualization.</description>
-   <requirements>
-      <requirement type="package" version="2019.7">qiime2</requirement>
-   </requirements>
-   <command><![CDATA[qiime tools export --input-path $isequences --output-path test && cd test && gunzip *]]></command>
-   <inputs>
-      <param format="qza,no_unzip.zip" label="Input artifact to export! [required]" name="isequences" optional="False" type="data" />
-   </inputs>
-
-   <outputs>
-      <collection type="paired" label="Export artifact to collection" name="output">
-         <discover_datasets pattern="__designation_and_ext__" directory="test" />
-      </collection>
-   </outputs>
-   <help />
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>
\ No newline at end of file
--- a/qiime2/qiime_tools_import.xml	Thu Sep 03 09:56:05 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,291 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_tools_import" name="qiime tools import" version="2019.7">
-	<description> - Import data into a new QIIME 2 Artifact.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command>
-<![CDATA[
-mkdir input;
-
-#set $in_= 'input'
-
-
-#if '__ob__' in str($semantic_type):
-	#set $type_temp = str($semantic_type).replace('__ob__', '[')
-	#set $type_temp = str($type_temp).replace('__cb__', ']')
-	#set $semantic_type = $type_temp
-#end if
-
-#def is_fastq($f_test)
-	#set $f = open($f_test, 'rb')
-	#set $fastq = str($f.readline()[0])
-	#if str($f.readline()[0]) == '@'
-		#$f.close()
-		#return True
-	#end if
-
-	#$f.close()
-	#return $fastq
-#end def
-
-
-## Symlinks creation or On the fly creation of a combo file
-#if $input_type.type == 'list_list'
-	## Symlinks creation or On the fly creation of a combo file
-	#for $f in $input_type.list_list:
-
-		#set $is_fastq_file = $is_fastq(str($f))			
-
-		#if $is_fastq_file:
-			#set $file_for_processing = "'input/" + $f.name + '.gz' + "'"
-			gzip -c ${f} > $file_for_processing;	
-			##echo $is_fastq_file;			
-		#else
-			#set $file_for_processing = "'input/" + $f.name + "'"
-			ln -s ${f}  $file_for_processing;	
-			##echo $is_fastq_file;
-		#end if
-	#end for
-	#if 'SingleEndFastqManifestPhred' in str($inputformat):
-			#set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
-			#set $tt = str("sample-id,absolute-filepath,direction")
-			echo $tt >> $cwf;
-			#for $f in $input_type.list_list:
-				#set $tt = str($f.name).split("_")[0]+",$PWD/input/"+str($f.name).split(".")[0]+".fastq.gz,forward\n"
-				echo $tt >> $cwf;	 
-			#end for
-			
-			#set $in_= str($cwf)
-		#end if
-	
-
-#elif $input_type.type == 'list_paired_collection':
-  
-	#set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
-	#set $tt = str("sample-id,absolute-filepath,direction")
-	echo $tt >> $cwf;
-
-	#for $pair in $input_type.list_paired_collection:
-		#set $forward_is_fastq_file = $is_fastq(str($pair.forward))
-		#set $reverse_is_fastq_file = $is_fastq(str($pair.reverse))
-		
-		#if $forward_is_fastq_file:
-	 		gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz;
-	 		#set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
-			echo $tt >> $cwf;			
-		#else
-	  		ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz;
-			#set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
-			echo $tt >> $cwf;		
-        #end if
-
-	 	#if $reverse_is_fastq_file:
-	 		gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz;
-			#set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
-			echo $tt >> $cwf;			
-        #else
-	  		ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz;
-			#set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
-			echo $tt >> $cwf;			
-	  	#end if
-	#end for
-
-	
-	
-	#if 'PairedEndFastqManifestPhred' in str($inputformat) or 'SingleEndFastqManifestPhred33V2' in str($inputformat) or 'SingleEndFastqManifestPhred33' in str($inputformat):
-		
-		#set $in_= str($cwf)
-		
-	#elif  'Casava' in str($inputformat):
-		#set $in_= 'input'
-	#end if
-
-	
-#else
-	#set $res = $is_fastq(str($file))
-
-	#if $res
-		gzip -c ${file} > ${file.name}.gz;
-		#set $in_= $file.name + '.gz'
-
-	#else
-		#set $in_= str($file)
-	#end if
-   
-   #if "MultiplexedSingleEndBarcodeInSequence" in str($semantic_type):      
- 			mv *_R1_* forward.fastq.gz;
-	    #set $in_= 'forward.fastq.gz';
-   #end if 
-
-#end if
-
-
-## rename files to predefined names for "MultiplexedPairedEndBarcodeInSequence"
-#if "MultiplexedPairedEndBarcodeInSequence" in str($semantic_type):
-		mv input/*_R1_* input/forward.fastq.gz;
-		mv input/*_R2_* input/reverse.fastq.gz;
-#end if
-
-
-qiime tools import
-
---input-path=$in_
-
-#if str($inputformat) != 'None':
-	#if '__ob__' in str($inputformat):
-  		#set $inputformat_temp = str($inputformat).replace('__ob__', '[')
-		#set $inputformat_temp = str($inputformat_temp).replace('__cb__', ']')
-  		#set $inputformat = $inputformat_temp
-	#end if
- --input-format="$inputformat"
-#end if
-
---type="$semantic_type"
-
---output-path=outputpath.qza
-
-;
-cp outputpath.qza $outputpath
-]]>
-	</command>
-	<inputs>
-		<conditional name="input_type">
-			<param name="type" type="select" label="Select a way to provide data, either using a file or a list" help="">
-				<option value="regular">Input file</option>
-                <option selected="true" value="list_paired_collection">Multiple pairs - Combo mode (list:paired collection)</option>
-				<option value="list_list">Input list</option>
-			</param>
-
-			<when value="regular">
-				<param name="file" type="data" multiple="false" label="Input file" />
-			</when>
-		 	<when value="list_paired_collection">
-            	<param name="list_paired_collection" type="data_collection" collection_type="list:paired" label="Fastq pairs (collection)" help="Dataset collection made from multiple pairs of files" />
-         	</when>
-			<when value="list_list">
-				<param name="list_list" type="data_collection" collection_type="list" label="Input list" />
-			</when>
-		</conditional>
-
-		<param label="--type: The semantic type of the artifact that will be created upon importing. [required]" name="semantic_type" optional="False" type="select">
-			<option value="DeblurStats">DeblurStats</option>
-			<option value="DistanceMatrix">DistanceMatrix</option>
-			<option value="EMPPairedEndSequences">EMPPairedEndSequences</option>
-			<option value="EMPSingleEndSequences">EMPSingleEndSequences</option>
-			<option value="ErrorCorrectionDetails">ErrorCorrectionDetails</option>
-			<option value="FeatureData[AlignedSequence]">FeatureData[AlignedSequence]</option>
-			<option value="FeatureData[Importance]">FeatureData[Importance]</option>
-			<option value="FeatureData[PairedEndSequence]">FeatureData[PairedEndSequence]</option>
-			<option value="FeatureData[Sequence]">FeatureData[Sequence]</option>
-			<option value="FeatureData[Taxonomy]">FeatureData[Taxonomy]</option>
-			<option value="FeatureTable[Balance]">FeatureTable[Balance]</option>
-			<option value="FeatureTable[Composition]">FeatureTable[Composition]</option>
-			<option value="FeatureTable[Frequency]">FeatureTable[Frequency]</option>
-			<option value="FeatureTable[PercentileNormalized]">FeatureTable[PercentileNormalized]</option>
-			<option value="FeatureTable[PresenceAbsence]">FeatureTable[PresenceAbsence]</option>
-			<option value="FeatureTable[RelativeFrequency]">FeatureTable[RelativeFrequency]</option>
-			<option value="Hierarchy">Hierarchy</option>
-			<option value="MultiplexedPairedEndBarcodeInSequence">MultiplexedPairedEndBarcodeInSequence</option>
-			<option value="MultiplexedSingleEndBarcodeInSequence">MultiplexedSingleEndBarcodeInSequence</option>
-			<option value="PCoAResults">PCoAResults</option>
-			<option value="Phylogeny[Rooted]">Phylogeny[Rooted]</option>
-			<option value="Phylogeny[Unrooted]">Phylogeny[Unrooted]</option>
-			<option value="Placements">Placements</option>
-			<option value="QualityFilterStats">QualityFilterStats</option>
-			<option value="RawSequences">RawSequences</option>
-			<option value="SampleData[AlphaDiversity]">SampleData[AlphaDiversity]</option>
-			<option value="SampleData[BooleanSeries]">SampleData[BooleanSeries]</option>
-			<option value="SampleData[ClassifierPredictions]">SampleData[ClassifierPredictions]</option>
-			<option value="SampleData[DADA2Stats]">SampleData[DADA2Stats]</option>
-			<option value="SampleData[FirstDifferences]">SampleData[FirstDifferences]</option>
-			<option value="SampleData[JoinedSequencesWithQuality]">SampleData[JoinedSequencesWithQuality]</option>
-			<option selected="True" value="SampleData[PairedEndSequencesWithQuality]">SampleData[PairedEndSequencesWithQuality]</option>
-			<option value="SampleData[RegressorPredictions]">SampleData[RegressorPredictions]</option>
-			<option value="SampleData[SequencesWithQuality]">SampleData[SequencesWithQuality]</option>
-			<option value="SampleData[Sequences]">SampleData[Sequences]</option>
-			<option value="SampleData[Classifier]">SampleData[Classifier]</option>
-			<option value="SampleData[Regressor]">SampleData[Regressor]</option>
-			<option value="TaxonomicClassifier">TaxonomicClassifier</option>
-			<option value="UchimeStats">UchimeStats</option>
-		</param>
-
-		<param label="--input-format: The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type." name="inputformat" optional="True" type="select">
-			<option value="AlignedDNAFASTAFormat">AlignedDNAFASTAFormat</option>
-			<option value="AlignedDNASequencesDirectoryFormat">AlignedDNASequencesDirectoryFormat</option>
-			<option value="AlphaDiversityDirectoryFormat">AlphaDiversityDirectoryFormat</option>
-			<option value="AlphaDiversityFormat">AlphaDiversityFormat</option>
-			<option value="BIOMV100DirFmt">BIOMV100DirFmt</option>
-			<option value="BIOMV100Format">BIOMV100Format</option>
-			<option value="BIOMV210DirFmt">BIOMV210DirFmt</option>
-			<option value="BIOMV210Format">BIOMV210Format</option>
-			<option value="BooleanSeriesDirectoryFormat">BooleanSeriesDirectoryFormat</option>
-			<option value="BooleanSeriesFormat">BooleanSeriesFormat</option>
-			<option value="CasavaOneEightLanelessPerSampleDirFmt">CasavaOneEightLanelessPerSampleDirFmt</option>
-			<option value="CasavaOneEightSingleLanePerSampleDirFmt">CasavaOneEightSingleLanePerSampleDirFmt</option>
-			<option value="DADA2StatsDirFmt">DADA2StatsDirFmt</option>
-			<option value="DADA2StatsFormat">DADA2StatsFormat</option>
-			<option value="DNAFASTAFormat">DNAFASTAFormat</option>
-			<option value="DNASequencesDirectoryFormat">DNASequencesDirectoryFormat</option>
-			<option value="DeblurStatsDirFmt">DeblurStatsDirFmt</option>
-			<option value="DeblurStatsFmt">DeblurStatsFmt</option>
-			<option value="DistanceMatrixDirectoryFormat">DistanceMatrixDirectoryFormat</option>
-			<option value="EMPPairedEndCasavaDirFmt">EMPPairedEndCasavaDirFmt</option>
-			<option value="EMPPairedEndDirFmt">EMPPairedEndDirFmt</option>
-			<option value="EMPSingleEndCasavaDirFmt">EMPSingleEndCasavaDirFmt</option>
-			<option value="EMPSingleEndDirFmt">EMPSingleEndDirFmt</option>
-			<option value="ErrorCorrectionDetailsDirFmt">ErrorCorrectionDetailsDirFmt</option>
-			<option value="FastqGzFormat">FastqGzFormat</option>
-			<option value="FirstDifferencesDirectoryFormat">FirstDifferencesDirectoryFormat</option>
-			<option value="FirstDifferencesFormat">FirstDifferencesFormat</option>
-			<option value="HeaderlessTSVTaxonomyDirectoryFormat">HeaderlessTSVTaxonomyDirectoryFormat</option>
-			<option value="HeaderlessTSVTaxonomyFormat">HeaderlessTSVTaxonomyFormat</option>
-			<option value="ImportanceDirectoryFormat">ImportanceDirectoryFormat</option>
-			<option value="ImportanceFormat">ImportanceFormat</option>
-			<option value="LSMatFormat">LSMatFormat</option>
-			<option value="MultiplexedPairedEndBarcodeInSequenceDirFmt">MultiplexedPairedEndBarcodeInSequenceDirFmt</option>
-			<option value="MultiplexedSingleEndBarcodeInSequenceDirFmt">MultiplexedSingleEndBarcodeInSequenceDirFmt</option>
-			<option value="NewickDirectoryFormat">NewickDirectoryFormat</option>
-			<option value="NewickFormat">NewickFormat</option>
-			<option value="OrdinationDirectoryFormat">OrdinationDirectoryFormat</option>
-			<option value="OrdinationFormat">OrdinationFormat</option>
-			<option value="PairedDNASequencesDirectoryFormat">PairedDNASequencesDirectoryFormat</option>
-			<option value="PairedEndFastqManifestPhred33">PairedEndFastqManifestPhred33</option>
-			<option value="PairedEndFastqManifestPhred33V2">PairedEndFastqManifestPhred33V2</option>
-			<option value="PairedEndFastqManifestPhred64">PairedEndFastqManifestPhred64</option>
-			<option value="PairedEndFastqManifestPhred64V2">PairedEndFastqManifestPhred64V2</option>
-			<option value="PlacementsDirFmt">PlacementsDirFmt</option>
-			<option value="PlacementsFormat">PlacementsFormat</option>
-			<option value="PredictionsDirectoryFormat">PredictionsDirectoryFormat</option>
-			<option value="PredictionsFormat">PredictionsFormat</option>
-			<option value="QIIME1DemuxDirFmt">QIIME1DemuxDirFmt</option>
-			<option value="QIIME1DemuxFormat">QIIME1DemuxFormat</option>
-			<option value="QualityFilterStatsDirFmt">QualityFilterStatsDirFmt</option>
-			<option value="QualityFilterStatsFmt">QualityFilterStatsFmt</option>
-			<option value="SampleEstimatorDirFmt">SampleEstimatorDirFmt</option>
-			<option value="SingleEndFastqManifestPhred33">SingleEndFastqManifestPhred33</option>
-			<option value="SingleEndFastqManifestPhred33V2">SingleEndFastqManifestPhred33V2</option>
-			<option value="SingleEndFastqManifestPhred64">SingleEndFastqManifestPhred64</option>
-			<option value="SingleEndFastqManifestPhred64V2">SingleEndFastqManifestPhred64V2</option>
-			<option value="SingleLanePerSamplePairedEndFastqDirFmt">SingleLanePerSamplePairedEndFastqDirFmt</option>
-			<option value="SingleLanePerSampleSingleEndFastqDirFmt">SingleLanePerSampleSingleEndFastqDirFmt</option>
-			<option value="TSVTaxonomyDirectoryFormat">TSVTaxonomyDirectoryFormat</option>
-			<option value="TSVTaxonomyFormat">TSVTaxonomyFormat</option>
-			<option value="TaxonomicClassiferTemporaryPickleDirFmt">TaxonomicClassiferTemporaryPickleDirFmt</option>
-			<option value="UchimeStatsDirFmt">UchimeStatsDirFmt</option>
-			<option value="UchimeStatsFmt">UchimeStatsFmt</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: outputpath.qza" name="outputpath"/>
-	</outputs>
-	    <!--<stdio>
-        <exit_code range="2"   level="warning"   description="Error" />
-    </stdio>-->
-	<help>
-</help>
-<macros>
-	<import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation" />
-</tool>