Mercurial > repos > iuc > arriba_get_filters
comparison macros.xml @ 5:703a2cb3fb38 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea
| author | iuc |
|---|---|
| date | Wed, 25 Oct 2023 08:24:19 +0000 |
| parents | 32e542c2a773 |
| children | 7a5a2d28c539 |
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| 4:32e542c2a773 | 5:703a2cb3fb38 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@TOOL_VERSION@">2.4.0</token> | 2 <token name="@TOOL_VERSION@">2.4.0</token> |
| 3 <token name="@VERSION_SUFFIX@">0</token> | 3 <token name="@VERSION_SUFFIX@">1</token> |
| 4 <xml name="requirements"> | 4 <xml name="requirements"> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> | 6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> |
| 7 <yield/> | 7 <yield/> |
| 8 </requirements> | 8 </requirements> |
| 51 #if $genome.assembly | 51 #if $genome.assembly |
| 52 #set $genome_assembly = 'genome.fa' | 52 #set $genome_assembly = 'genome.fa' |
| 53 ln -sf '$genome.assembly' $genome_assembly && | 53 ln -sf '$genome.assembly' $genome_assembly && |
| 54 #end if | 54 #end if |
| 55 #elif str($genome.genome_source) == "cached" | 55 #elif str($genome.genome_source) == "cached" |
| 56 #set $genome_assembly = $genome.ref_file.fields.fasta | 56 #set $genome_assembly = $genome.ref_file.fields.path |
| 57 #end if | 57 #end if |
| 58 ]]></token> | 58 ]]></token> |
| 59 <token name="@GTF_SOURCE@"><![CDATA[ | 59 <token name="@GTF_SOURCE@"><![CDATA[ |
| 60 #if str($genome_gtf.gtf_source) == "history" | 60 #if str($genome_gtf.gtf_source) == "history" |
| 61 ln -sf '$genome_gtf.annotation' genome.gtf && | 61 ln -sf '$genome_gtf.annotation' genome.gtf && |
| 62 #end if | 62 #end if |
| 63 ]]></token> | 63 ]]></token> |
| 64 | 64 |
| 65 <xml name="visualization_options"> | 65 <xml name="visualization_options"> |
| 66 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> | 66 <param argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> |
| 67 <section name="options" expanded="false" title="Draw Fusion Options"> | 67 <section name="options" expanded="false" title="Draw Fusion Options"> |
| 68 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> | 68 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> |
| 69 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> | 69 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> |
| 70 <help>By default the transcript isoform with the highest coverage is drawn. | 70 <help>By default the transcript isoform with the highest coverage is drawn. |
| 71 Alternatively, the transcript isoform that is provided in the columns | 71 Alternatively, the transcript isoform that is provided in the columns |