Mercurial > repos > charles_s_test > test_dependencies
changeset 1:09e4f955e00a draft
planemo upload commit d4d558b27a09f684be8311f3cfb659b16545e167-dirty
| author | charles_s_test |
|---|---|
| date | Sun, 12 Nov 2017 09:14:07 -0500 |
| parents | 500ceb70e4bd |
| children | aca83a94fd55 |
| files | fastq_dump_paired.xml |
| diffstat | 1 files changed, 0 insertions(+), 54 deletions(-) [+] |
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--- a/fastq_dump_paired.xml Sun Nov 12 09:12:36 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<tool id="testdep" name="Test Dep" version="1.1.4"> - <description>Downloads a set of paired reads by their accession number using fastq-dump tool from sra-toolkit.</description> - <requirements> - <!-- Should just use the samtools that's installed in the path --> - <requirement type="binary">fastq-dump</requirement> - </requirements> - <command interpreter="python2.7"> - - testdep.py ${input1} - - </command> - <inputs> - <param format="fastq,fastqsanger" name="input1" multiple="true" type="data" label="Source file"/> - </inputs> - <outputs> - <data name="text_file" format="txt" from_work_dir="dep_result.txt"/> - - </outputs> - <tests> - <!-- Empty --> - </tests> - - <help> - -.. class:: infomark - -**What it does** - -Performs a fastq-dump with the split-3 option. - -:: - - fastq-dump —log-level fatal --split-3 --accession accession_number --ncbi_error_report never - - -Data is stored in format fastqsanger. - -The metadata is now named to make it easier for collection lists to -fetch when you search for reads in your history. - ------- - -.. class:: infomark - -Modifed By -Charles Strittmatter - - -**Original Tool Author** - -Mando Rodriguez - - </help> -</tool>