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comparison fastq_dump_paired.xml @ 0:4a455773d235 draft

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author mandorodriguez
date Mon, 28 Sep 2015 12:53:10 -0400
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1 <tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.0">
2 <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
3 <requirements>
4 <!-- Should just use the samtools that's installed in the path -->
5 <requirement type="binary">fastq-dump</requirement>
6 </requirements>
7 <command>
8 ## The command is a Cheetah template which allows some Python based syntax.
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
10 ## ! We only have a simple single command here.
11 fastq-dump --log-level fatal --split-3 --accession ${accession_number};
12 ls -lh | grep ${accession_number};
13 mv -v ${accession_number}_1.fastq R1.fastq;
14 mv -v ${accession_number}_2.fastq R2.fastq;
15 </command>
16 <inputs>
17 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
18 </inputs>
19 <outputs>
20 <data format="fastq" label="${tool.name} on ${on_string}: Forward Reads" name="forward_reads" from_work_dir="R1.fastq" >
21 </data>
22 <data format="fastq" label="${tool.name} on ${on_string}: Reverse Reads" name="reverse_reads" from_work_dir="R2.fastq" >
23 </data>
24 </outputs>
25
26 <tests>
27 <!-- Empty -->
28 </tests>
29
30 <help>
31
32 .. class:: infomark
33
34 **What it does**
35
36 Performs a fastq-dump with the split-3 option.
37
38 ::
39
40 fastq-dump --log-level fatal --split-3 --accession accession_number
41
42 ------
43
44 .. class:: infomark
45
46 **Tool Author**
47
48 Mando Rodriguez
49
50 </help>
51 </tool>