diff qiime2/qiime_tools_import.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_tools_import.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_tools_import.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -19,13 +19,14 @@
 
 #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 False
+	#return $fastq
 #end def
 
 
@@ -34,33 +35,36 @@
 	## 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))
+		#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;
+			gzip -c ${f} > $file_for_processing;	
+			##echo $is_fastq_file;			
 		#else
 			#set $file_for_processing = "'input/" + $f.name + "'"
-			ln -s ${f}  $file_for_processing;
+			ln -s ${f}  $file_for_processing;	
+			##echo $is_fastq_file;
 		#end if
 	#end for
 	#if 'SingleEndFastqManifestPhred' in str($inputformat):
-			#set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
-			#set $m_file = open(str($cwd), 'w')
-			$m_file.write("sample-id,absolute-filepath,direction\n")
+			#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:
-				$m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n")
+				#set $tt = str($f.name).split("_")[0]+",$PWD/input/"+str($f.name).split(".")[0]+".fastq.gz,forward\n"
+				echo $tt >> $cwf;	 
 			#end for
-			$m_file.close()
-			#set $in_= str($cwd)
+			
+			#set $in_= str($cwf)
 		#end if
 	
 
 #elif $input_type.type == 'list_paired_collection':
   
-	#set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt"
-	#set $m_file = open(str($cwd), 'w')
-	$m_file.write("sample-id,absolute-filepath,direction\n")	
+	#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))
@@ -68,29 +72,36 @@
 		
 		#if $forward_is_fastq_file:
 	 		gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz;
-	 		$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n")
+	 		#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;
-			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n")
+			#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;
-			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n")
+			#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;
-			$m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n")
+			#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
 
 	
-	$m_file.close()
-	#if 'PairedEndFastqManifestPhred' in str($inputformat):
-		#set $in_= str($cwd)
+	
+	#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))
 
@@ -268,9 +279,9 @@
 	<outputs>
 		<data format="qza" label="${tool.name} on ${on_string}: outputpath.qza" name="outputpath"/>
 	</outputs>
-	    <stdio>
+	    <!--<stdio>
         <exit_code range="2"   level="warning"   description="Error" />
-    </stdio>
+    </stdio>-->
 	<help>
 </help>
 <macros>