Mercurial > repos > iuc > arriba_draw_fusions
comparison macros.xml @ 5:cf01dd6c6b1f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea
author | iuc |
---|---|
date | Wed, 25 Oct 2023 08:24:28 +0000 |
parents | 31f8063eedea |
children | 7acb00fc980a |
comparison
equal
deleted
inserted
replaced
4:31f8063eedea | 5:cf01dd6c6b1f |
---|---|
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 |