diff fastq_dump.xml @ 2:f256cb398262 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026

--- a/fastq_dump.xml	Tue May 17 14:14:50 2016 -0400
+++ b/fastq_dump.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Extract reads" version="1.3.0">
+<tool id="fastq_dump" name="Extract reads" version="2.6.2">
     <description>in FASTQ/A format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -21,10 +21,10 @@
     #if $input.input_select=="file_list" or $input.input_select=="accession_number":
           [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
     #end if
-    
+
     ## Need to set the home directory to the current working directory,
-    ## else the tool tries to write to home/.ncbi and fails when used 
-    ## with a cluster manager. 
+    ## else the tool tries to write to home/.ncbi and fails when used
+    ## with a cluster manager.
     export HOME=\$PWD &&
     vdb-config --restore-defaults &&
     #if $input.input_select == "file":
@@ -76,7 +76,7 @@
     #end if
     $adv.clip
     $adv.skip_technical
-    
+
     #if str( $outputformat ) == "fasta":
         --fasta
     #end if
@@ -97,15 +97,15 @@
 
 
     #if str( $outputformat ) == "fasta":
-    
+
         for f in *_2.fasta ; do   mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ;  mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta"  ; done &&
         for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
-        
+
     #else:
 
         for f in *_2.fastq ; do   mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ;  mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq"  ; done &&
         for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
-        
+
     #end if
 
 
@@ -114,7 +114,7 @@
 
     #end if
 
-    
+
     ]]>
     </command>
     <inputs>
@@ -202,7 +202,7 @@
         This tool extracts reads from SRA archives using fastq-dump.
         The fastq-dump program is developed at NCBI, and is available at
         http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-        
+
         NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
         @SRATOOLS_ATTRRIBUTION@
     </help>