Mercurial > repos > jfallmann > aresite2
changeset 0:52d2bcae95e2 draft
Uploaded xml
author | jfallmann |
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date | Wed, 01 Feb 2017 09:54:15 -0500 |
parents | |
children | 6e02034384c7 |
files | aresite2.xml |
diffstat | 1 files changed, 53 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aresite2.xml Wed Feb 01 09:54:15 2017 -0500 @@ -0,0 +1,53 @@ +<tool id="AREsite2_REST" name="Get motifs from AREsite2" version="0.1.2"> + <description>AREsite2 REST Interface</description> + <requirements> + <requirement type="package" version="2.12.4">requests</requirement> + <requirement type="package" version="1.10.0">six</requirement> + </requirements> + <command> +<![CDATA[ +python $__tool_directory__/aresite2.py +-g $gene +-m "$motif" +-s $species_selector +> $AREsite2_REST_out +]]> + </command> + + <inputs> + <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" /> + <param name="species_selector" type="select" label="Select species"> + <option value="Homo_sapiens" selected="true"></option> + <option value="Mus_musculus"></option> + <option value="Danio_rerio"></option> + <option value="Drosophila_melanogaster"></option> + <option value="Caenorhabditis_elegans"></option> + </param> + <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" /> + </inputs> + + <outputs> + <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" type="text" format="bed" /> + </outputs> + + <tests> + <test> + <param name="species" value="Homo_sapiens" /> + <param name="motif" value="ATTTA" /> + <param name="gene" value="Cxcl2" /> + <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" /> + </test> + </tests> + + <help> +<![CDATA[ +**What it does** + +Retrieve motif information in BED format from AREsite2 using its REST API. + +]]> + </help> + <citations> + <citation type="doi">10.1093/nar/gkv1238</citation> + </citations> +</tool>