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comparison junction_annotation.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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59:dbedfc5f5a3c 60:1421603cc95b
1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>compares detected splice junctions to reference gene model</description> 2 <description>compares detected splice junctions to reference gene model</description>
3 <expand macro="bio_tools"/> 3 <expand macro="bio_tools"/>
4 <macros> 4 <macros>
5 <import>rseqc_macros.xml</import> 5 <import>rseqc_macros.xml</import>
6 </macros> 6 </macros>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <!-- 9 <!--
10 Required due to conda solver bug: https://github.com/conda/conda/issues/6269 10 Required due to conda solver bug: https://github.com/conda/conda/issues/6269
11 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info 11 See: https://github.com/galaxyproject/tools-iuc/pull/1578 for more info
12 --> 12 -->
13 <requirement type="package" version="3.4.1">r-base</requirement> 13 <requirement type="package" version="4.2.2">r-base</requirement>
14 </expand> 14 </expand>
15 15
16 <expand macro="stdio" /> 16 <expand macro="stdio" />
17 17
18 <version_command><![CDATA[junction_annotation.py --version]]></version_command> 18 <version_command><![CDATA[junction_annotation.py --version]]></version_command>
19 19
20 <command><![CDATA[ 20 <command><![CDATA[
21 @BAM_SAM_INPUTS@
21 junction_annotation.py 22 junction_annotation.py
22 --input-file '${input}' 23 --input-file 'input.${extension}'
23 --refgene '${refgene}' 24 --refgene '${refgene}'
24 --out-prefix output 25 --out-prefix output
25 --min-intron ${min_intron} 26 --min-intron ${min_intron}
26 --mapq ${mapq} 27 --mapq ${mapq}
27 ]]> 28 ]]>