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comparison fastq_dump.xml @ 2:6aa2efbe5920 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
author iuc
date Fri, 16 Sep 2016 17:23:44 -0400
parents 069a879beef7
children 62367c99119d
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1:069a879beef7 2:6aa2efbe5920
1 <tool id="fastq_dump" name="Extract reads" version="1.3.0"> 1 <tool id="fastq_dump" name="Extract reads" version="2.6.2">
2 <description>in FASTQ/A format from NCBI SRA.</description> 2 <description>in FASTQ/A 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"/>
19 #end if 19 #end if
20 20
21 #if $input.input_select=="file_list" or $input.input_select=="accession_number": 21 #if $input.input_select=="file_list" or $input.input_select=="accession_number":
22 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( 22 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
23 #end if 23 #end if
24 24
25 ## Need to set the home directory to the current working directory, 25 ## Need to set the home directory to the current working directory,
26 ## else the tool tries to write to home/.ncbi and fails when used 26 ## else the tool tries to write to home/.ncbi and fails when used
27 ## with a cluster manager. 27 ## with a cluster manager.
28 export HOME=\$PWD && 28 export HOME=\$PWD &&
29 vdb-config --restore-defaults && 29 vdb-config --restore-defaults &&
30 #if $input.input_select == "file": 30 #if $input.input_select == "file":
31 fastq-dump --log-level fatal --accession '${input.file.name}' 31 fastq-dump --log-level fatal --accession '${input.file.name}'
32 #else: 32 #else:
74 #if str( $adv.matepairDist ) != "": 74 #if str( $adv.matepairDist ) != "":
75 --matepair-distance "$adv.matepairDist" 75 --matepair-distance "$adv.matepairDist"
76 #end if 76 #end if
77 $adv.clip 77 $adv.clip
78 $adv.skip_technical 78 $adv.skip_technical
79 79
80 #if str( $outputformat ) == "fasta": 80 #if str( $outputformat ) == "fasta":
81 --fasta 81 --fasta
82 #end if 82 #end if
83 #if $input.input_select=="file": 83 #if $input.input_select=="file":
84 --stdout 84 --stdout
95 95
96 ; 96 ;
97 97
98 98
99 #if str( $outputformat ) == "fasta": 99 #if str( $outputformat ) == "fasta":
100 100
101 for f in *_2.fasta ; do mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ; mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta" ; done && 101 for f in *_2.fasta ; do mv "\$f" "`basename \$f _2.fasta`_reverse.fasta" ; mv "`basename \$f _2.fasta`_1.fasta" "`basename \$f _2.fasta`_forward.fasta" ; done &&
102 for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done 102 for f in *_1.fasta; do mv "\$f" "`basename \$f _1.fasta`__single.fasta"; done
103 103
104 #else: 104 #else:
105 105
106 for f in *_2.fastq ; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ; mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq" ; done && 106 for f in *_2.fastq ; do mv "\$f" "`basename \$f _2.fastq`_reverse.fastq" ; mv "`basename \$f _2.fastq`_1.fastq" "`basename \$f _2.fastq`_forward.fastq" ; done &&
107 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done 107 for f in *_1.fastq; do mv "\$f" "`basename \$f _1.fastq`__single.fastq"; done
108 108
109 #end if 109 #end if
110 110
111 111
112 112
113 113
114 114
115 #end if 115 #end if
116 116
117 117
118 ]]> 118 ]]>
119 </command> 119 </command>
120 <inputs> 120 <inputs>
121 <expand macro="input_conditional"/> 121 <expand macro="input_conditional"/>
122 <param name="outputformat" type="select" label="select output format"> 122 <param name="outputformat" type="select" label="select output format">
200 </tests> 200 </tests>
201 <help> 201 <help>
202 This tool extracts reads from SRA archives using fastq-dump. 202 This tool extracts reads from SRA archives using fastq-dump.
203 The fastq-dump program is developed at NCBI, and is available at 203 The fastq-dump program is developed at NCBI, and is available at
204 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. 204 http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
205 205
206 NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively 206 NB: Single-end or pair-end collections may be empty if given SRRs LibraryLayout contains only either SINGLE or PAIRED respectively
207 @SRATOOLS_ATTRRIBUTION@ 207 @SRATOOLS_ATTRRIBUTION@
208 </help> 208 </help>
209 <expand macro="citation"/> 209 <expand macro="citation"/>
210 </tool> 210 </tool>