diff fastq_dump.xml @ 16:aad3885b3216 draft

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

--- a/fastq_dump.xml	Tue Sep 10 11:35:35 2019 -0400
+++ b/fastq_dump.xml	Fri Mar 20 12:47:18 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.4">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,14 +6,12 @@
     <expand macro="requirements"/>
     <version_command>fastq-dump --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-
     @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.
-    export HOME=\$PWD &&
-    vdb-config --restore-defaults &&
+    @CONFIGURE_TIMEOUT@
     #if $input.input_select == "file":
         fastq-dump --log-level fatal --accession '${input.file.name}'
     #else:
@@ -21,9 +19,7 @@
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
         #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
-            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" &&