sra_tools: fastq_dump.xml annotate

annotate fastq_dump.xml @ 9:6c60903f70ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd

author	iuc
date	Wed, 12 Jul 2017 00:48:56 -0400
parents	1920e0508831
children	c38286ea7047

rev	line source
9 6c60903f70ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 6252dc2340b2fb6c7fdab2bdadfa4779c6f1aefd iuc parents: 8 diff changeset	1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3">
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	2 <description>format from NCBI SRA</description>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	3 <macros>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	4 <import>sra_macros.xml</import>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	5 </macros>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	6 <expand macro="requirements"/>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	7 <version_command>fastq-dump --version</version_command>
4 62e4d56ebb6f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4091428e9e28ca06263bc00cdf938d20f620aa4d iuc parents: 3 diff changeset	8 <command detect_errors="exit_code">
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	9 <![CDATA[
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	10
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	11 #if $input.input_select=="file_list":
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	12
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	13 for acc in `cat $input.file_list` ;
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	14 do
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	15
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	16 #elif $input.input_select=="accession_number":
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	17
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	18 ## Stripping leading and trailing spaces in case user typed them in
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	19 acc="${input.accession}" &&
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	20
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	21 #end if
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	22
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	23 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	24
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	25 [ ""\$acc" =~ ^[E\|S\|D]RR[0-9]{1,}$" ] && (
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	26
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	27 #end if
2 f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	28
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	29 ## Need to set the home directory to the current working directory,
2 f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	30 ## else the tool tries to write to home/.ncbi and fails when used
f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	31 ## with a cluster manager.
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	32 export HOME=\$PWD &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	33 vdb-config --restore-defaults &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	34 #if $input.input_select == "file":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	35 fastq-dump --log-level fatal --accession '${input.file.name}'
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	36 #else:
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	37 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	38 ## Do not use prefetch if region is specified, to avoid downloading
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	39 ## the complete sra file.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	40 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	41 ASCP_PATH=`command -v ascp` &&
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	42 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh \|\| true &&
3 4732693f4661 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd iuc parents: 2 diff changeset	43 prefetch -X 200G --ascp-path "\$ASCP_PATH\|\$ASCP_KEY" "\$acc" &&
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	44 ## Duplicate vdb-config, in case settings changed between prefetch and
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	45 ## dump command.
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	46 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	47 #end if
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	48 fastq-dump --accession "\$acc"
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	49 --split-files
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	50 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	51 --defline-seq '@\$sn[_\$rn]/\$ri'
8 1920e0508831 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 39ca11da7daeb3fa030fcb28e8987f8d7f24aec3 iuc parents: 7 diff changeset	52 --defline-qual '+'
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	53
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	54 $adv.split
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	55 #if str( $adv.alignments ) == "aligned":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	56 --aligned
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	57 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	58 #if str( $adv.alignments ) == "unaligned":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	59 --unaligned
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	60 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	61 #if str( $adv.minID ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	62 --minSpotId "$adv.minID"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	63 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	64 #if str( $adv.maxID ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	65 --maxSpotId "$adv.maxID"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	66 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	67 #if str( $adv.minlen ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	68 --minReadLen "$adv.minlen"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	69 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	70 #if str( $adv.readfilter ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	71 --read-filter "$adv.readfilter"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	72 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	73 #if str( $adv.region ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	74 --aligned-region "$adv.region"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	75 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	76 #if str( $adv.spotgroups ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	77 --spot-groups "$adv.spotgroups"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	78 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	79 #if str( $adv.matepairDist ) != "":
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	80 --matepair-distance "$adv.matepairDist"
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	81 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	82 $adv.clip
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	83 $adv.skip_technical
2 f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	84
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	85 #if str( $outputformat ) == "fastqsanger.gz":
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	86 --gzip
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	87 #elif str( $outputformat ) == "fastqsanger.bz2":
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	88 --bzip2
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	89 #end if
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	90 #if $input.input_select=="file":
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	91 --stdout
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	92 "$input.file" > "$output_file"
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	93
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	94 #elif $input.input_select=="accession_number":
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	95 --stdout
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	96 "\$acc" > "$output_accession" )
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	97 #end if
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	98
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	99 #if $input.input_select=="file_list":
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	100 ) ; done
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	101
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	102 ;
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	103
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	104 for i in `ls .fast \| cut -f 1 -d '_' \| uniq` ; do
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	105 count=`ls \$i* \| wc -l` ;
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	106 data=(\$(ls -d \$i*));
6 30775c836c77 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ee50324111351323cc294e051a6fab1733a89ec1 iuc parents: 4 diff changeset	107
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	108 if [ "\$count" -eq 2 ]; then
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	109 mv "\${data[0]}" "\${data[0]}"_forward.$outputformat; mv "\${data[1]}" "\${data[1]}"_reverse.$outputformat ;
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	110 elif [ "\$count" -eq 1 ]; then
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	111 mv "\${data[0]}" "\${data[0]}"__single.$outputformat ;
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	112 fi;
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	113 done
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	114
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	115
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	116 #end if
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	117
2 f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	118
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	119 ]]>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	120 </command>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	121 <inputs>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	122 <expand macro="input_conditional"/>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	123 <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">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	124 <option value="fastqsanger.gz">gzip compressed fastq</option>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	125 <option value="fastqsanger">Uncompressed fastq</option>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	126 <option value="fastqsanger.bz2">bzip2 compressed fastq</option>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	127 </param>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	128 <section name="adv" title="Advanced Options" expanded="False">
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	129 <param name="minID" type="integer" label="Minimum spot ID" optional="true" help="Minimum spot id to be dumped." argument="--minSpotId"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	130 <param name="maxID" type="integer" label="Maximum spot ID" optional="true" help="Maximum spot id to be dumped." argument="--maxSpotId"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	131 <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--minReadLen"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	132 <param name="split" type="boolean" checked="true" truevalue="--split-spot" falsevalue="" label="Split spot by read pairs" help="Split spots into individual reads." argument="--split-spot"/>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	133 <expand macro="alignments"/>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	134 <expand macro="region"/>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	135 <expand macro="matepairDist"/>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	136 <param name="readfilter" type="select" value="" label="filter by value" argument="--read-filter">
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	137 <option value="">None</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	138 <option value="pass">pass</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	139 <option value="reject">reject</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	140 <option value="criteria">criteria</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	141 <option value="redacted">redacted</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	142 </param>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	143 <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	144 <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	145 <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	146 </section>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	147 </inputs>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	148 <outputs>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	149 <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	150 <filter>input['input_select'] == "file_list"</filter>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	151
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	152 <!-- Use named regex group to grab pattern
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	153 <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	154 identifier in the nested collection and identifier_1 is either
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	155 forward or reverse (for instance samp1_forward.fq).
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	156 -->
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	157
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	158 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq_(?P<identifier_1>[^_]+)\.fastqsanger" ext="fastqsanger" />
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	159 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq.gz_(?P<identifier_1>[^_]+)\.fastqsanger.gz" ext="fastqsanger.gz" />
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	160 <discover_datasets pattern="(?P<identifier_0>[^_]+)_\d+.fastq.bz2_(?P<identifier_1>[^_]+)\.fastqsanger.bz2" ext="fastqsanger.bz2" />
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	161 </collection>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	162 <collection name="output_collection" type='list' label="Single-end data (fastq-dump)">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	163 <filter>input['input_select'] == "file_list"</filter>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	164 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq__single\.fastqsanger" directory="." ext='fastqsanger'/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	165 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq.gz__single\.fastqsanger.gz" directory="." ext='fastqsanger.gz'/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	166 <discover_datasets pattern="(?P<designation>.+)_\d+.fastq.bz2__single\.fastqsanger.bz2" directory="." ext='fastqsanger.bz2'/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	167 </collection>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	168 <data format="fastqsanger" name="output_accession" label="${input.accession} (fastq-dump)">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	169 <filter>input['input_select'] == "accession_number"</filter>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	170 <change_format>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	171 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	172 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	173 </change_format>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	174 </data>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	175 <data format="fastqsanger" name="output_file" label="${input.file.name} (fastq-dump)">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	176 <filter>input['input_select'] == "file"</filter>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	177 <change_format>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	178 <when input="outputformat" value="fastqsanger.gz" format="fastqsanger.gz"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	179 <when input="outputformat" value="fastqsanger.bz2" format="fastqsanger.bz2"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	180 </change_format>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	181 </data>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	182 </outputs>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	183 <tests>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	184 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	185 <param name="input_select" value="accession_number"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	186 <param name="outputformat" value="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	187 <param name="accession" value="SRR044777"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	188 <param name="skip_technical" value="True"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	189 <output name="output_accession">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	190 <assert_contents>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	191 <not_has_text text="rRNA_primer"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	192 <has_text text="F47USSH02GNP1D" />
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	193 </assert_contents>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	194 </output>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	195 </test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	196 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	197 <param name="input_select" value="accession_number"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	198 <param name="outputformat" value="fastqsanger.gz"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	199 <param name="accession" value="SRR925743"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	200 <param name="maxID" value="5"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	201 <output name="output_accession" file="fastq_dump_result.fastq.gz" decompress="True"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	202 </test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	203 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	204 <param name="input_select" value="accession_number"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	205 <param name="outputformat" value="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	206 <param name="accession" value="SRR925743"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	207 <param name="maxID" value="5"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	208 <output name="output_accession" file="fastq_dump_result.fastq" ftype="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	209 </test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	210 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	211 <param name="input_select" value="file_list"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	212 <param name="outputformat" value="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	213 <param name="file_list" value="list_pe"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	214 <param name="maxID" value="5"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	215 <output_collection name="list_paired" type="list:paired">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	216 <element name="DRR015708">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	217 <element name="forward" file="DRR015708_forward.fastqsanger">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	218 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	219 <element name="reverse" file="DRR015708_reverse.fastqsanger">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	220 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	221 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	222 </output_collection>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	223 </test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	224 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	225 <param name="input_select" value="file_list"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	226 <param name="outputformat" value="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	227 <param name="file_list" value="list_pe2"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	228 <param name="maxID" value="5"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	229 <output_collection name="list_paired" type="list:paired">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	230 <element name="ERR027433">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	231 <element name="forward" file="ERR027433_forward.fastqsanger">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	232 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	233 <element name="reverse" file="ERR027433_reverse.fastqsanger">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	234 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	235 </element>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	236 </output_collection>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	237 </test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	238 <test>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	239 <param name="input_select" value="file_list"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	240 <param name="outputformat" value="fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	241 <param name="file_list" value="list_se"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	242 <param name="maxID" value="5"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	243 <output_collection name="output_collection" type="list">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	244 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	245 </output_collection>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	246 </test>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	247 </tests>
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	248 <help><![CDATA[
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	249 What it does?
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	250
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	251 This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fastq-dump_ utility of the SRA Toolkit.
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	252
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	253 How to use it?
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	254
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	255 There are three ways in which you can download data:
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	256
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	257 1. Data for single accession
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	258 2. Multiple datasets using a list of accessions
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	259 3. Extract data from already uploaded SRA dataset
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	260
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	261 Below we discuss each in detail.
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	262
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	263 ------
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	264
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	265 Uploading data for a single accession
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	266
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	267 When you type a single accession number (e.g., `SRR1582967`) into Accession box and click Execute the tool will fetch data for you. It is important to keep the following in mind:
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	268
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	269 - if data is paired-ended (or mate-paired) the tool will generate a single interleaved dataset, in which forward and reverse mates are alternating (see an example dataset below)
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	270 - if data is single ended, a standard single fastq dataset will be produced
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	271
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	272 -----
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	273
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	274 Uploading multiple datasets using a list of accessions
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	275
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	276 A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	277
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	278 1. Upload it into your history using Galaxy's upload tool
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	279 2. Once the list of accessions is uploaded choose List of SRA accessions, one per line from select input type dropdown
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	280 3. Choose uploaded file within the sra accession list field
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	281 4. Click Execute
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	282
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	283 .. class:: warningmark
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	284
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	285 Fastq datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. In fact, two collections will be produced: one containing paired-end data and another containing single-end data. Single-end or pair-end collections may be empty if the accessions provided in the list contain only SINGLE or PAIRED data, respectively.
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	286
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	287 -----
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	288
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	289 Extract data from already uploaded SRA dataset
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	290
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	291 If a SRA dataset is present in the history, it can be converted into fastq dataset by setting select input type drop-down to SRA archive in current history. Just like in the case of extracting data for single accession number the following applies:
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	292
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	293 - if data is paired-ended (or mate-pair) the tool will generate a single interleaved dataset, in which forward and reverse mates are alternating (see example below).
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	294 - if data is single ended, a standard fastq dataset will be produced
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	295
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	296 @ACCESSION_LIST_HOWTO@
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c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	298 -----
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	299
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	300 Paired-end (and mate-pair) data in fastq format
2 f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026 iuc parents: 1 diff changeset	301
7 c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	302 Paired end datasets can be represented as two individual datasets:
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	303
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	304 First dataset::
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	305
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	306 @1/1
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	307 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	308 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	309 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	310 @2/1
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	311 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	312 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	313 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	314
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	315 Second dataset::
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	316
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	317 @1/2
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	318 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	319 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	320 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	321 @2/2
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	322 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	323 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	324 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	325
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	326 Or a single interleaved dataset::
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	327
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	328 @1/1
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	329 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	330 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	331 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	332 @1/2
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	333 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	334 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	335 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	336 @2/1
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	337 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	338 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	339 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	340 @2/2
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	341 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	342 +
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	343 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	344
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	345 ----
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	346
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	347
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	348 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	349 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	350 .. _collection: https://galaxyproject.org/tutorials/collections/
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	351 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	352
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	353 @SRATOOLS_ATTRRIBUTION@
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	354
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1 iuc parents: 6 diff changeset	355 ]]>
0 b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	356 </help>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297 iuc parents: diff changeset	357 <expand macro="citation"/>
1 462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede iuc parents: 0 diff changeset	358 </tool>

Mercurial > repos > iuc > sra_tools

annotate fastq_dump.xml @ 9:6c60903f70ac draft