Mercurial > repos > iuc > sra_tools

diff fastq_dump.xml @ 13:c38286ea7047 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91
author iuc
date Wed, 17 Oct 2018 11:44:12 -0400
parents 6c60903f70ac
children f5ea3ce9b9b0
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line diff
--- a/fastq_dump.xml	Wed Sep 26 05:33:56 2018 -0400
+++ b/fastq_dump.xml	Wed Oct 17 11:44:12 2018 -0400
@@ -5,26 +5,9 @@
     </macros>
     <expand macro="requirements"/>
     <version_command>fastq-dump --version</version_command>
-    <command detect_errors="exit_code">
-        <![CDATA[
-
-    #if $input.input_select=="file_list":
-    
-        for acc in `cat $input.file_list` ;
-        do
-    
-    #elif $input.input_select=="accession_number":
+    <command detect_errors="exit_code"><![CDATA[
 
-        ## Stripping leading and trailing spaces in case user typed them in 
-        acc="${input.accession}" &&
-    
-    #end if
-
-    #if $input.input_select=="file_list" or $input.input_select=="accession_number":
-    
-        [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
-    
-    #end if
+    @SET_ACCESSIONS@
 
     ## Need to set the home directory to the current working directory,
     ## else the tool tries to write to home/.ncbi and fails when used