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comparison sam_dump.xml @ 3:62367c99119d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
author iuc
date Tue, 18 Oct 2016 14:54:14 -0400
parents 6aa2efbe5920
children de3b6a854c0a
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2:6aa2efbe5920 3:62367c99119d
1 <tool id="sam_dump" name="Extract reads" version="2.6.2"> 1 <tool id="sam_dump" name="Extract reads" version="@VERSION@">
2 <description>in SAM or BAM format from NCBI SRA.</description> 2 <description>in SAM or BAM 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"/>
29 ## Do not use prefetch if region is specified, to avoid downloading 29 ## Do not use prefetch if region is specified, to avoid downloading
30 ## the complete sra file. 30 ## the complete sra file.
31 #if ( str( $adv.region ) == "" ): 31 #if ( str( $adv.region ) == "" ):
32 ASCP_PATH=`command -v ascp` && 32 ASCP_PATH=`command -v ascp` &&
33 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && 33 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
34 prefetch --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && 34 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
35 ## Duplicate vdb-config, in case settings changed between prefetch and 35 ## Duplicate vdb-config, in case settings changed between prefetch and
36 ## dump command. 36 ## dump command.
37 vdb-config -s "/repository/user/main/public/root=\$PWD" && 37 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
38 #end if 38 #end if
39 sam-dump --log-level fatal --disable-multithreading 39 sam-dump --log-level fatal --disable-multithreading