Mercurial > repos > iuc > arriba_draw_fusions

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
author iuc
date Wed, 25 Sep 2024 15:30:11 +0000
parents 2d4e3aff9dc7
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2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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1 <tool id="arriba_draw_fusions" name="Arriba Draw Fusions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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2 <description></description>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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3 <macros>
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iuc
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4 <import>macros.xml</import>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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5 </macros>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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6 <expand macro="requirements" />
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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7 <expand macro="version_command" />
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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8 <command detect_errors="exit_code"><![CDATA[
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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9 #if $alignments.extension == 'sam'
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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10 ln -sf '$genome.assembly' genome.fa &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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11 samtools faidx genome.fa &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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12 samtools view -b -@ \${GALAXY_SLOTS:-1} -t genome.fa.fai '$alignments' |
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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13 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o Aligned.sortedByCoord.out.bam &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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14 samtools index Aligned.sortedByCoord.out.bam &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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15 #else
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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16 ln -sf '${alignments}' 'Aligned.sortedByCoord.out.bam' &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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17 ln -sf '$alignments.metadata.bam_index' 'Aligned.sortedByCoord.out.bam.bai' &&
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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18 #end if
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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19 @DRAW_FUSIONS@
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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20 ]]></command>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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21 <inputs>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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22 <param argument="--fusions" type="data" format="tabular" label="Arriba fusions.tsv"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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23 <param argument="--alignments" type="data" format="sam,bam" label="STAR Aligned.out.bam"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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24 <expand macro="genome_source" assembly_optional="true"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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25 <expand macro="gtf_source"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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26 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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27 <section name="visualization" expanded="true" title="Visualization Options">
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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28 <expand macro="visualization_options" />
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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29 </section>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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30 </inputs>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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31 <outputs>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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32 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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33 </outputs>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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34 <tests>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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35 <!-- Test 1 - From SAM -->
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36 <test>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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37 <param name="fusions" ftype="tabular" value="fusions.tsv"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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38 <param name="alignments" ftype="sam" value="Aligned.out.sam"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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39 <conditional name="genome">
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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40 <param name="genome_source" value="history"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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41 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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42 </conditional>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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43 <conditional name="genome_gtf">
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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44 <param name="gtf_source" value="history"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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45 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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46 </conditional>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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47 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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48 <section name="visualization">
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49 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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50 </section>
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51 <output name="fusions_pdf">
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52 <assert_contents>
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53 <has_size value="64000" delta="5000" />
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54 </assert_contents>
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55 </output>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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56 </test>
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57 <!-- Test 2 - From BAM -->
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58 <test>
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59 <param name="fusions" ftype="tabular" value="fusions.tsv"/>
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60 <param name="alignments" ftype="bam" value="Aligned.out.bam"/>
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61 <conditional name="genome">
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62 <param name="genome_source" value="history"/>
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63 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
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64 </conditional>
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65 <conditional name="genome_gtf">
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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66 <param name="gtf_source" value="history"/>
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67 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
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68 </conditional>
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69 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
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70 <section name="visualization">
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71 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
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72 </section>
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73 <section name="options">
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74 <param name="sampleName" value="My Test"/>
2d4e3aff9dc7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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75 </section>
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76 <output name="fusions_pdf">
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77 <assert_contents>
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78 <has_size value="64000" delta="5000" />
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79 </assert_contents>
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80 </output>
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81 </test>
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82
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83 </tests>
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84 <help><![CDATA[
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85 **Arriba Draw Fusions**
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86
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87 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.
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88
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89
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90 **INPUTS**
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91
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92 See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
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93
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94 - Fusions
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95
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96 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).
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97
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98 - Annotation
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99
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100 Gene annotation in GTF format that was used by the STAR aligner.
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101
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102 - Alignments
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103
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104 BAM file containing normal alignments from STAR.
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105
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106 - Annotation
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107
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108 The gene annotation (parameter -g) is used for multiple purposes:
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109
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110 - Assembly (Optional)
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111
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112 Only required when alignments are not sorted bam format. The genonme assembly will be used by samtools to produce a sorted bam file.
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113
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114 - Protein domains (Optional)
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115
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116 GFF3 file containing the genomic coordinates of protein domains. Distributions of Arriba offer protein domain annotations for all supported assemblies in the database directory. When this file is given, a plot is generated, which shows the protein domains retained in the fusion transcript.
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117
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118 - Cytobands (Optional)
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119
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120 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.
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121
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122
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123 **OPTIONS**
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124
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125 See: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
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126
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127
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128 **OUTPUTS**
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129
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130 See: https://arriba.readthedocs.io/en/latest/visualization/
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131
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132 - fusions.pdf
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133
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134 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.
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135
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136 .. image:: draw-fusions-example.png
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137 :width: 800
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138 :height: 467
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139
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140
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141
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142
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143 .. _Arriba_Draw_Fusions: https://arriba.readthedocs.io/en/latest/visualization/
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144 .. _Arriba: https://arriba.readthedocs.io/en/latest/
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145
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146 ]]></help>
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147 <expand macro="citations" />
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148 </tool>