Mercurial > repos > iuc > sra_tools

diff sam_dump.xml @ 2:f256cb398262 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author iuc
date Fri, 16 Sep 2016 17:24:03 -0400
parents 462ee06c9358
children 4732693f4661
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--- a/sam_dump.xml	Tue May 17 14:14:50 2016 -0400
+++ b/sam_dump.xml	Fri Sep 16 17:24:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Extract reads" version="1.3.0">
+<tool id="sam_dump" name="Extract reads" version="2.6.2">
     <description>in SAM or BAM format from NCBI SRA.</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -21,8 +21,8 @@
 
 
         ## 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 &&
         vdb-config -s "/repository/user/main/public/root=\$PWD" &&
@@ -67,7 +67,7 @@
         #elif $input.input_select=="file_list":
             "\$acc"
         #end if
-        
+
         #if str( $outputformat ) == "bam":
             | samtools view -Sb - 2> /dev/null
         #end if
@@ -117,7 +117,7 @@
           <filter>input['input_select'] == "file_list"</filter>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="." ext='bam'/>
           <discover_datasets pattern="(?P&lt;designation&gt;.+)\.sam" directory="." ext='sam'/>
-        </collection>      
+        </collection>
         <data name="output_accession" format="bam" label="${input.accession}.${outputformat}">
             <filter>input['input_select'] == "accession_number"</filter>
             <change_format>