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comparison fastq_dump.xml @ 16:aad3885b3216 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"
author iuc
date Fri, 20 Mar 2020 12:47:18 -0400
parents f5ea3ce9b9b0
children 7068f48d0ef9
comparison
equal deleted inserted replaced
15:f5ea3ce9b9b0 16:aad3885b3216
1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.4"> 1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>fastq-dump --version</version_command> 7 <version_command>fastq-dump --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
10 @SET_ACCESSIONS@ 9 @SET_ACCESSIONS@
11 10
12 ## Need to set the home directory to the current working directory, 11 ## Need to set the home directory to the current working directory,
13 ## else the tool tries to write to home/.ncbi and fails when used 12 ## else the tool tries to write to home/.ncbi and fails when used
14 ## with a cluster manager. 13 ## with a cluster manager.
15 export HOME=\$PWD && 14 @CONFIGURE_TIMEOUT@
16 vdb-config --restore-defaults &&
17 #if $input.input_select == "file": 15 #if $input.input_select == "file":
18 fastq-dump --log-level fatal --accession '${input.file.name}' 16 fastq-dump --log-level fatal --accession '${input.file.name}'
19 #else: 17 #else:
20 vdb-config -s "/repository/user/main/public/root=\$PWD" && 18 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
21 ## Do not use prefetch if region is specified, to avoid downloading 19 ## Do not use prefetch if region is specified, to avoid downloading
22 ## the complete sra file. 20 ## the complete sra file.
23 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): 21 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
24 ASCP_PATH=`command -v ascp` && 22 prefetch -X 200000000 "\$acc" &&
25 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
26 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
27 ## Duplicate vdb-config, in case settings changed between prefetch and 23 ## Duplicate vdb-config, in case settings changed between prefetch and
28 ## dump command. 24 ## dump command.
29 vdb-config -s "/repository/user/main/public/root=\$PWD" && 25 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
30 #end if 26 #end if
31 fastq-dump --accession "\$acc" 27 fastq-dump --accession "\$acc"