comparison arriba_draw_fusions.xml @ 7:24271361028f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0

6:7acb00fc980a

Arriba_Draw_Fusions_ (draw_fusions.R) renders publication-quality visualizations of the transcripts involved in predicted fusions. It generates a PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and - if the column fusion_transcript has a value - an excerpt of the sequence around the breakpoint.


**INPUTS**

See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr

  - Fusions  

    File containing fusion predictions from Arriba_ (fusions.tsv) or STAR-Fusion (star-fusion.fusion_predictions.tsv or star-fusion.fusion_predictions.abridged.coding_effect.tsv).

    Coordinates of the Giemsa staining bands. This information is used to draw ideograms. If the argument is omitted, then no ideograms are rendered. The file must have the following columns: contig, start, end, name, giemsa. Recognized values for the Giemsa staining intensity are: gneg, gpos followed by a percentage, acen, stalk. Cytobands forahuman and mouse reference can be retrieved from the Arriba distribution with the **Arriba Get Filters** tool. 


**OPTIONS**

  See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr


**OUTPUTS**

See: https://arriba.readthedocs.io/en/latest/visualization/

  - fusions.pdf

    A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.

  :height: 467




.. _Arriba_Draw_Fusions: https://arriba.readthedocs.io/en/latest/visualization/
.. _Arriba: https://arriba.readthedocs.io/en/latest/

    ]]></help>
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7:24271361028f

Arriba_Draw_Fusions_ (draw_fusions.R) renders publication-quality visualizations of the transcripts involved in predicted fusions. It generates a PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and - if the column fusion_transcript has a value - an excerpt of the sequence around the breakpoint.


**INPUTS**

See: https://github.com/suhrig/arriba/wiki/07-Command-line-options#draw_fusionsr

  - Fusions  

    File containing fusion predictions from Arriba_ (fusions.tsv) or STAR-Fusion (star-fusion.fusion_predictions.tsv or star-fusion.fusion_predictions.abridged.coding_effect.tsv).

    Coordinates of the Giemsa staining bands. This information is used to draw ideograms. If the argument is omitted, then no ideograms are rendered. The file must have the following columns: contig, start, end, name, giemsa. Recognized values for the Giemsa staining intensity are: gneg, gpos followed by a percentage, acen, stalk. Cytobands forahuman and mouse reference can be retrieved from the Arriba distribution with the **Arriba Get Filters** tool. 


**OPTIONS**

  See: https://github.com/suhrig/arriba/wiki/07-Command-line-options#draw_fusionsr


**OUTPUTS**

See: https://github.com/suhrig/arriba/wiki/06-Visualization

  - fusions.pdf

    A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.

  :height: 467




.. _Arriba_Draw_Fusions: https://github.com/suhrig/arriba/wiki/06-Visualization
.. _Arriba: https://github.com/suhrig/arriba/wiki/01-Home

    ]]></help>
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</tool>