Mercurial > repos > yhoogstrate > fuma
diff fuma.xml @ 9:b21145d59d9c draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/fuma commit 7bf6f3629e96bcaaed8770badd11366889efa99c
| author | erasmusmc |
|---|---|
| date | Mon, 23 Jan 2017 09:41:08 -0500 |
| parents | 8366a8c82a7a |
| children |
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--- a/fuma.xml Mon Feb 08 04:56:40 2016 -0500 +++ b/fuma.xml Mon Jan 23 09:41:08 2017 -0500 @@ -1,14 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="fuma" name="FuMa" version="2.11.3-g0"> +<tool id="fuma" name="FuMa" version="3.0.5-g0"> <description>match detected fusion genes based on gene names (in particular for RNA-Seq)</description> - + <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="2.11.3">fuma</requirement> + <requirement type="package" version="3.0.5">fuma</requirement> </requirements> - + <version_command>fuma --version 2>&1 | head -n 1</version_command><!-- -V also works, but is not GNU standard --> - + <command><![CDATA[ #import pipes @@ -25,9 +24,9 @@ #set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ] #end for - #set $gene_annotations_str = " ".join(gene_annotations) - #set $samples_str = " ".join(samples) - #set $links_str = " ".join(links) + #set $gene_annotations_str = "'"+"' '".join(gene_annotations)+"'" + #set $samples_str = "'"+"' '".join(samples)+"'" + #set $links_str = "'"+"' '".join(links)+"'" fuma -m @@ -49,12 +48,12 @@ #else -f $params.output_format.value #end if - -o $fuma_overview ; + -o '${fuma_overview}' #if $params.output_format.value == "list_boolean" - fuma-list-to-boolean-list -o tmp.txt $fuma_overview ; - mv tmp.txt $fuma_overview + && fuma-list-to-boolean-list -o tmp.txt '${fuma_overview}' + && mv tmp.txt '${fuma_overview}' #end if ]]></command> @@ -94,7 +93,9 @@ <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"> + <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" + argument="-m"> <option value="overlap">Overlap</option> <option value="subset" selected="True">Subset</option> <option value="egm">Exact Geneset Matching (EGM)</option> @@ -111,7 +112,9 @@ 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="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" + argument="--long-gene-size" /> <param name="output_format" type="select" label="Output format"> <option value="list_boolean" selected="true">List (Boolean)</option> @@ -127,27 +130,70 @@ </outputs> <tests> + <!-- Large tests, take long <test> - <!-- <repeat name="datasets"> --> - <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> - <param name="datasets_0|format" value="chimerascan" /> - <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> - <param name="datasets_1|format" value="defuse" /> - <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" /> - <param name="datasets_2|format" value="fusionmap" /> - <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" /> - <param name="datasets_3|format" value="fusionmap" /> - <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> + <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> + <param name="datasets_0|format" value="chimerascan" /> + <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> + <param name="datasets_1|format" value="defuse" /> + <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" /> + <param name="datasets_2|format" value="fusionmap" /> + <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" /> + <param name="datasets_3|format" value="fusionmap" /> + <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="settingsType" value="full" /> + + <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" /> + </test> + <test> + <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" /> + <param name="datasets_0|format" value="fusionmap" /> + <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" /> + <param name="datasets_1|format" value="fusionmap" /> + <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> + <param name="datasets_0|format" value="chimerascan" /> + <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> + <param name="datasets_1|format" value="defuse" /> + <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="settingsType" value="full" /> + + <param name="matching_method" value="subset" /> + <param name="strand_specific_matching" value="False" /> + <param name="acceptor_donor_order_specific_matchig" value="False" /> + <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" /> + </test> + --> + <test> + <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" /> + <param name="datasets_0|format" value="fusionmap" /> + <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" /> + <param name="datasets_1|format" value="fusionmap" /> + <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <param name="settingsType" value="full" /> @@ -157,29 +203,16 @@ <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" /> + <output name="fuma_overview" file="edgren_test_03_specific_matching_output.txt" /> </test> <test> - <!-- <repeat name="datasets"> --> - <param name="datasets_0|sample" value="edgren_chimerascan.txt" ftype="tabular" /> - <param name="datasets_0|format" value="chimerascan" /> - <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_1|sample" value="edgren_defuse.txt" ftype="tabular" /> - <param name="datasets_1|format" value="defuse" /> - <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_2|sample" value="edgren_fusion-map.txt" ftype="tabular" /> - <param name="datasets_2|format" value="fusionmap" /> - <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> - <!-- <repeat name="datasets"> --> - <param name="datasets_3|sample" value="edgren_true_positives.txt" ftype="tabular" /> - <param name="datasets_3|format" value="fusionmap" /> - <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> - <!-- </repeat> --> + <param name="datasets_0|sample" value="edgren_fusion-map.txt" ftype="tabular" /> + <param name="datasets_0|format" value="fusionmap" /> + <param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> + + <param name="datasets_1|sample" value="edgren_true_positives.txt" ftype="tabular" /> + <param name="datasets_1|format" value="fusionmap" /> + <param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" /> <param name="settingsType" value="full" /> @@ -189,7 +222,7 @@ <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" /> + <output name="fuma_overview" file="edgren_test_04_unspecific_matching_output.txt" /> </test> </tests>