diff sam_dump.xml @ 16:aad3885b3216 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"

--- a/sam_dump.xml	Tue Sep 10 11:35:35 2019 -0400
+++ b/sam_dump.xml	Fri Mar 20 12:47:18 2020 -0400
@@ -1,9 +1,11 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.10">samtools</requirement>
+    </expand>
     <version_command>sam-dump --version</version_command>
     <command detect_errors="exit_code">
 <![CDATA[
@@ -12,8 +14,7 @@
         ## 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.
-        export HOME=\$PWD &&
-        vdb-config --restore-defaults &&
+        @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.
@@ -22,9 +23,7 @@
             sam-dump --log-level fatal  '${input.file.name}'
         #else:
             #if ( str( $adv.region ) == "" ):
-                ASCP_PATH=`command -v ascp` &&
-                ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-                prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+                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" &&