Mercurial > repos > yhoogstrate > fuma
changeset 10:d39811cb7c3a draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
| author | yhoogstrate |
|---|---|
| date | Fri, 20 Nov 2015 11:14:23 -0500 |
| parents | 77abea4fc3e7 |
| children | 666993f510c6 |
| files | fuma.xml |
| diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/fuma.xml Fri Nov 20 11:01:04 2015 -0500 +++ b/fuma.xml Fri Nov 20 11:14:23 2015 -0500 @@ -36,6 +36,8 @@ $params.strand_specific_matching $params.acceptor_donor_order_specific_matchig + --long-gene-size $params.long_gene_size + -a $gene_annotations_str -s @@ -85,7 +87,8 @@ </param> <when value="preSet"> <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" /> - <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--acceptor-donor-order-specific-matching" /> + <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--no-acceptor-donor-order-specific-matching" /> + <param name="long_gene_size" type="hidden" value="200000" /> </when> <when value="full"> <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative"> @@ -97,7 +100,7 @@ <param name="strand_specific_matching" type="boolean" checked="True" truevalue="--strand-specific-matching" falsevalue="--no-strand-specific-matching" - label="Consider fusion genes distinct when the breakpoints have different strands: (A<-,B<) != (->A,B<-); default" + label="Consider fusion genes distinct when the breakpoints have different strands: (A<-,B<-) != (->A,B<-); default" help="Only a limited number of file formats support this feature" /> <param name="acceptor_donor_order_specific_matchig" type="boolean" checked="False" truevalue="--acceptor-donor-order-specific-matching" @@ -105,6 +108,8 @@ label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)" help="This settings is not recommended when fusion genes detected in DNA-Seq are used" /> + <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size" help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a 'long gene' as reported the output. Use 0 to disable this feature (--long-gene-size)" /> + <param name="output_format" type="select" label="Output format"> <option value="list_boolean" selected="true">List (Boolean)</option> <option value="list">List</option> @@ -146,6 +151,7 @@ <param name="matching_method" value="subset" /> <param name="strand_specific_matching" value="--strand-specific-matching" /> <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" /> + <param name="long_gene_size" value="200000" /> <param name="output_format" value="list_boolean" /> <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" /> @@ -177,6 +183,7 @@ <param name="matching_method" value="subset" /> <param name="strand_specific_matching" value="False" /><!-- Set to false, automatically sets the false value --> <param name="acceptor_donor_order_specific_matchig" value="False" /><!-- Set to false, automatically sets the false value --> + <param name="long_gene_size" value="200000" /> <param name="output_format" value="list_boolean" /> <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />