bioproject_to_srr_2: bio2srr.xml annotate

planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538

rev	line source
jpayne@4	1 <tool id="bio2srr" name="Bioproject to SRR" version="3.0.0">
jpayne@4	2 <description>Retrieve SRR accessions and sample metadata from BioProject. Recursively follows links to subprojects.</description>
jpayne@0	3 <requirements>
jpayne@6	4 <container type="docker">crashfrog/bio2srr</container>
jpayne@0	5 </requirements>
jpayne@0	6 <command detect_errors="exit_code"><![CDATA[
jpayne@4	7 python $__tool_directory__/bio2srr.py "$input1"
jpayne@0	8 ]]></command>
jpayne@0	9 <inputs>
jpayne@4	10 <param type="text" name="input1" label="BioProject" />
jpayne@0	11 </inputs>
jpayne@0	12 <outputs>
jpayne@4	13 <data format="txt" name="output" from_work_dir="accessions.txt" label="SRR Accession List" />
jpayne@2	14 <data format="tabular" name="metadata" from_work_dir="metadata.tsv" label="Sample Metadata Table" />
jpayne@0	15 </outputs>
jpayne@0	16 <tests>
jpayne@0	17 <test>
jpayne@4	18 <param name="input1" value="PRJNA681235" />
jpayne@4	19 <output name="output" file="accessions.txt" />
jpayne@2	20 <output name="metadata" file="metadata.tsv" />
jpayne@0	21 </test>
jpayne@4	22 <test expect_failure="1">
jpayne@4	23 <param name="input1" value="NOTHING" />
jpayne@4	24 </test>
jpayne@0	25 </tests>
jpayne@0	26 <help><![CDATA[
jpayne@4	27 Retrieve SRR accessions and sample metadata from a BioProject, including subprojects. It's a JOIN, so if a sample is associated with multiple SRA runs, then each run has a copy of the sample's metadata.
jpayne@0	28 ]]></help>
jpayne@0	29 <citations>
jpayne@0	30 </citations>
jpayne@0	31 </tool>

Mercurial > repos > jpayne > bioproject_to_srr_2