diff sam_dump.xml @ 18:7068f48d0ef9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"

--- a/sam_dump.xml	Wed Apr 29 12:12:23 2020 -0400
+++ b/sam_dump.xml	Mon Jun 08 05:49:21 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -9,13 +9,9 @@
     <version_command>sam-dump --version</version_command>
     <command detect_errors="exit_code">
 <![CDATA[
+        @COPY_CONFIGFILE@
         @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
-        ## with a cluster manager.
-        @CONFIGURE_TIMEOUT@
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
 
@@ -24,9 +20,6 @@
         #else:
             #if ( str( $adv.region ) == "" ):
                 prefetch -X 200000000 "\$acc" &&
-                ## Duplicate vdb-config, in case settings changed between prefetch and
-                ## dump command.
-                vdb-config -s "/repository/user/main/public/root=\$PWD" &&
             #end if
             sam-dump --log-level fatal --disable-multithreading
         #end if
@@ -79,6 +72,7 @@
 
         ]]>
     </command>
+    <expand macro="configfile_hack"/>
     <inputs>
         <expand macro="input_conditional"/>
         <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools.">
@@ -173,9 +167,9 @@
 -----
 
 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
-.. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html
+.. _sam-dump: https://ncbi.github.io/sra-tools/sam-dump.html
 .. _collection: https://galaxyproject.org/tutorials/collections/
-.. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
+.. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
 
 @SRATOOLS_ATTRRIBUTION@
     ]]></help>