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comparison fastq_dump_paired.xml @ 4:6c9eb322892d draft

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author mandorodriguez
date Wed, 28 Oct 2015 17:43:11 -0400
parents b3e5722aa5e7
children 86e30bb1e54e
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3:b3e5722aa5e7 4:6c9eb322892d
1 <tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1"> 1 <tool id="fastq_dump_paired" name="FASTQ Dump paired downloader" version="1.1.1">
2 <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description> 2 <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description>
3 <requirements> 3 <requirements>
4 <!-- Should just use the samtools that's installed in the path --> 4 <!-- Should just use the samtools that's installed in the path -->
5 <requirement type="binary">fastq-dump</requirement> 5 <requirement type="binary">fastq-dump</requirement>
6 </requirements> 6 </requirements>
15 </command> 15 </command>
16 <inputs> 16 <inputs>
17 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/> 17 <param name="accession_number" size="10" type="text" value="" label="Accession Number"/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data format="fastqsanger" label="${tool.name} on ${on_string}: ${accession_number} Forward Reads" name="forward_reads" from_work_dir="R1.fastq" > 20 <data format="fastqsanger" label="${accession_number}_1" name="forward_reads" from_work_dir="R1.fastq" >
21 </data> 21 </data>
22 <data format="fastqsanger" label="${tool.name} on ${on_string}: ${accession_number} Reverse Reads" name="reverse_reads" from_work_dir="R2.fastq" > 22 <data format="fastqsanger" label="${accession_number}_2" name="reverse_reads" from_work_dir="R2.fastq" >
23 </data> 23 </data>
24 </outputs> 24 </outputs>
25 25
26 <tests> 26 <tests>
27 <!-- Empty --> 27 <!-- Empty -->
38 :: 38 ::
39 39
40 fastq-dump --log-level fatal --split-3 --accession accession_number 40 fastq-dump --log-level fatal --split-3 --accession accession_number
41 41
42 42
43 Data is stored in fastqsanger format. 43 Data is stored in fastqsanger format.
44
45 The metadata is now named to make it easier for collection lists to
46 fetch when you search for reads in your history.
44 47
45 ------ 48 ------
46 49
47 .. class:: infomark 50 .. class:: infomark
48 51