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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit d90385601350b4d5fafae3004b470dee4a7f442d-dirty |
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modified:
fuma.xml tool_dependencies.xml |
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| diff -r ec04b7552167 -r 8366a8c82a7a fuma.xml --- a/fuma.xml Wed Dec 09 09:56:41 2015 -0500 +++ b/fuma.xml Mon Feb 08 04:56:40 2016 -0500 |
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| @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="fuma" name="FuMa" version="2.11.0.a"> +<tool id="fuma" name="FuMa" version="2.11.3-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="2.11.0">fuma</requirement> + <requirement type="package" version="2.11.3">fuma</requirement> </requirements> <version_command>fuma --version 2>&1 | head -n 1</version_command><!-- -V also works, but is not GNU standard --> @@ -64,12 +64,15 @@ <param name="format" type="select" label="Format of dataset"> <option value="chimera">Chimera prettyPrint()</option> <option value="chimerascan">ChimeraScan</option> + <option value="complete-genomics">Complete Genomics var/mastervar</option> <option value="defuse">DeFuse</option> - <option value="complete-genomics">Complete Genomics var/mastervar</option> + <option value="ericscript">EricScript (.results.total.txt)</option> <option value="fusion-catcher_final">Fusion Catcher (final-list file)</option> <option value="fusionmap">FusionMap</option> <option value="trinity-gmap">GMAP (As step after Trinity)</option> <option value="oncofuse">OncoFuse</option> + <option value="soapfuse-final-gene">SOAPFuse (final.*.for.genes.txt)</option> + <option value="soapfuse-final-transcript">SOAPFuse (final.*.for.trans.txt)</option> <option value="rna-star_chimeric">STAR (chimeric file)</option> <option value="star-fusion_final">STAR-Fusion (candidates.final)</option> <option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option> @@ -224,6 +227,8 @@ +-------------------+-----------------------+-------------------------------------+ |DeFuse | results.filtered.txt | defuse | +-------------------+-----------------------+-------------------------------------+ +|EricScript | .results.total.txt | ericscript ************* | ++-------------------+-----------------------+-------------------------------------+ |Fusion Catcher | final-list_cand*.txt | fusion-catcher_final | +-------------------+-----------------------+-------------------------------------+ |FusionMap | | fusionmap | @@ -234,6 +239,10 @@ +-------------------+-----------------------+-------------------------------------+ |RNA STAR | Chimeric.out.junction | rna-star_chimeric | +-------------------+-----------------------+-------------------------------------+ +|SOAPFuse | final.*.for.genes.txt | soapfuse-final-gene | ++-------------------+-----------------------+-------------------------------------+ +|SOAPFuse | final.*.for.trans.txt | soapfuse-final-transcript | ++-------------------+-----------------------+-------------------------------------+ |STAR Fusion | _candidates.final | star-fusion_final | +-------------------+-----------------------+-------------------------------------+ |TopHat Fusion pre | fusions.out | tophat-fusion_pre | @@ -245,6 +254,12 @@ |TopHat Fusion post | result.html | tophat-fusion_post_result_html | +-------------------+-----------------------+-------------------------------------+ +************* EricScript often contains entries with unknown breakpoints. +Because no genomic coordinates are given those fusion genes can not be +imported into FuMa and only those with breakpoints will be taken into account. + + + To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons. UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser. |
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| diff -r ec04b7552167 -r 8366a8c82a7a tool_dependencies.xml --- a/tool_dependencies.xml Wed Dec 09 09:56:41 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 08 04:56:40 2016 -0500 |
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| @@ -4,6 +4,6 @@ <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="fuma" version="2.11.0"> - <repository changeset_revision="f922f018f507" name="package_fuma_2_11_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="58d6b3e8bf1c" name="package_fuma_2_11_3" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |