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comparison sam_dump.xml @ 15:54366e4d692a 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 16:36:52 +0000
parents 5c5d6624f8de
children 37f09413ddbf
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14:5c5d6624f8de 15:54366e4d692a
1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4"> 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" 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 <requirement type="package" version="1.10">samtools</requirement>
8 </expand>
7 <version_command>sam-dump --version</version_command> 9 <version_command>sam-dump --version</version_command>
8 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
9 <![CDATA[ 11 <![CDATA[
10 @SET_ACCESSIONS@ 12 @SET_ACCESSIONS@
11 13
12 ## Need to set the home directory to the current working directory, 14 ## 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 15 ## else the tool tries to write to home/.ncbi and fails when used
14 ## with a cluster manager. 16 ## with a cluster manager.
15 export HOME=\$PWD && 17 @CONFIGURE_TIMEOUT@
16 vdb-config --restore-defaults &&
17 vdb-config -s "/repository/user/main/public/root=\$PWD" && 18 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
18 ## Do not use prefetch if region is specified, to avoid downloading 19 ## Do not use prefetch if region is specified, to avoid downloading
19 ## the complete sra file. 20 ## the complete sra file.
20 21
21 #if $input.input_select == "file": 22 #if $input.input_select == "file":
22 sam-dump --log-level fatal '${input.file.name}' 23 sam-dump --log-level fatal '${input.file.name}'
23 #else: 24 #else:
24 #if ( str( $adv.region ) == "" ): 25 #if ( str( $adv.region ) == "" ):
25 ASCP_PATH=`command -v ascp` && 26 prefetch -X 200000000 "\$acc" &&
26 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
27 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
28 ## Duplicate vdb-config, in case settings changed between prefetch and 27 ## Duplicate vdb-config, in case settings changed between prefetch and
29 ## dump command. 28 ## dump command.
30 vdb-config -s "/repository/user/main/public/root=\$PWD" && 29 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
31 #end if 30 #end if
32 sam-dump --log-level fatal --disable-multithreading 31 sam-dump --log-level fatal --disable-multithreading