diff fastq_dump.xml @ 18:7068f48d0ef9 draft

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

--- a/fastq_dump.xml	Wed Apr 29 12:12:23 2020 -0400
+++ b/fastq_dump.xml	Mon Jun 08 05:49:21 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,23 +6,16 @@
     <expand macro="requirements"/>
     <version_command>fastq-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@
     #if $input.input_select == "file":
         fastq-dump --log-level fatal --accession '${input.file.name}'
     #else:
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
         ## 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 ) == "" ):
             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
         fastq-dump --accession "\$acc"
         --split-files
@@ -104,6 +97,7 @@
 
     ]]>
     </command>
+    <expand macro="configfile_hack"/>
     <inputs>
         <expand macro="input_conditional"/>
         <param name="outputformat" type="select" display="radio" label="Select output format" help="Compression will greatly reduce the amount of space occupied by downloaded data. Downstream applications such as a short-read mappers will accept compressed data as input. Consider this example: an uncoimpressed 400 Mb fastq datasets compresses to 100 Mb or 80 Mb by gzip or bzip2, respectively. " argument="--gzip --bzip2">
@@ -343,7 +337,7 @@
 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-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@