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 2d69e621036bf155e02189d4a9a8aa9ee24536e0
author iuc
date Fri, 04 Apr 2025 10:37:40 +0000
parents 6dcdd899d135
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6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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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">
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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6 <expand macro="requirements" />
6dcdd899d135 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" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $alignments.extension == 'sam'
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10 ln -sf '$genome.assembly' genome.fa &&
6dcdd899d135 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 &&
6dcdd899d135 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 '$alignments' |
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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13 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o Aligned.sortedByCoord.out.bam &&
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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14 samtools index Aligned.sortedByCoord.out.bam &&
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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15 #else
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16 ln -sf '${alignments}' 'Aligned.sortedByCoord.out.bam' &&
6dcdd899d135 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' &&
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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18 #end if
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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19 @DRAW_FUSIONS@
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20 ]]></command>
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21 <inputs>
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22 <param argument="--fusions" type="data" format="tabular" label="Arriba fusions.tsv"/>
6dcdd899d135 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"/>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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24 <expand macro="genome_source" assembly_optional="true"/>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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25 <expand macro="gtf_source"/>
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26 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
6dcdd899d135 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">
6dcdd899d135 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" />
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29 </section>
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30 </inputs>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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31 <outputs>
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32 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"/>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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33 </outputs>
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34 <tests>
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35 <!-- Test 1 - From SAM -->
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36 <test>
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37 <param name="fusions" ftype="tabular" value="fusions.tsv"/>
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38 <param name="alignments" ftype="sam" value="Aligned.out.sam"/>
6dcdd899d135 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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39 <conditional name="genome">
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40 <param name="genome_source" value="history"/>
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41 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
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42 </conditional>
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43 <conditional name="genome_gtf">
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44 <param name="gtf_source" value="history"/>
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45 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
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46 </conditional>
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47 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
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48 <section name="visualization">
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49 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
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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>
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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">
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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"/>
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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://github.com/suhrig/arriba/wiki/07-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://github.com/suhrig/arriba/wiki/07-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://github.com/suhrig/arriba/wiki/06-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://github.com/suhrig/arriba/wiki/06-Visualization
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144 .. _Arriba: https://github.com/suhrig/arriba/wiki/01-Home
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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>