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comparison fastq_dump.xml @ 17:37f09413ddbf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author iuc
date Mon, 08 Jun 2020 09:48:56 +0000
parents 54366e4d692a
children c8d04fc889f2
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16:f61761f373ea 17:37f09413ddbf
1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01"> 1 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" 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 @COPY_CONFIGFILE@
9 @SET_ACCESSIONS@ 10 @SET_ACCESSIONS@
10 11
11 ## Need to set the home directory to the current working directory,
12 ## else the tool tries to write to home/.ncbi and fails when used
13 ## with a cluster manager.
14 @CONFIGURE_TIMEOUT@
15 #if $input.input_select == "file": 12 #if $input.input_select == "file":
16 fastq-dump --log-level fatal --accession '${input.file.name}' 13 fastq-dump --log-level fatal --accession '${input.file.name}'
17 #else: 14 #else:
18 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
19 ## Do not use prefetch if region is specified, to avoid downloading 15 ## Do not use prefetch if region is specified, to avoid downloading
20 ## the complete sra file. 16 ## the complete sra file.
21 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ): 17 #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
22 prefetch -X 200000000 "\$acc" && 18 prefetch -X 200000000 "\$acc" &&
23 ## Duplicate vdb-config, in case settings changed between prefetch and
24 ## dump command.
25 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
26 #end if 19 #end if
27 fastq-dump --accession "\$acc" 20 fastq-dump --accession "\$acc"
28 --split-files 21 --split-files
29 #end if 22 #end if
30 --defline-seq '@\$sn[_\$rn]/\$ri' 23 --defline-seq '@\$sn[_\$rn]/\$ri'
102 #end if 95 #end if
103 96
104 97
105 ]]> 98 ]]>
106 </command> 99 </command>
100 <expand macro="configfile_hack"/>
107 <inputs> 101 <inputs>
108 <expand macro="input_conditional"/> 102 <expand macro="input_conditional"/>
109 <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"> 103 <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">
110 <option value="fastqsanger.gz">gzip compressed fastq</option> 104 <option value="fastqsanger.gz">gzip compressed fastq</option>
111 <option value="fastqsanger">Uncompressed fastq</option> 105 <option value="fastqsanger">Uncompressed fastq</option>
341 335
342 336
343 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format 337 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
344 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html 338 .. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
345 .. _collection: https://galaxyproject.org/tutorials/collections/ 339 .. _collection: https://galaxyproject.org/tutorials/collections/
346 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies 340 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
347 341
348 @SRATOOLS_ATTRRIBUTION@ 342 @SRATOOLS_ATTRRIBUTION@
349 343
350 ]]> 344 ]]>
351 </help> 345 </help>