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comparison junction_saturation.xml @ 13:a7f9084572fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:21:47 +0000
parents 57fad5deeb8e
children
comparison
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12:57fad5deeb8e 13:a7f9084572fe
1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>detects splice junctions from each subset and compares them to reference gene model</description> 2 <description>detects splice junctions from each subset and compares them to reference gene model</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
6 </macros> 5 </macros>
7 6 <expand macro="bio_tools"/>
8 <expand macro="requirements" /> 7 <expand macro="requirements" />
9
10 <expand macro="stdio" /> 8 <expand macro="stdio" />
11
12 <version_command><![CDATA[junction_saturation.py --version]]></version_command> 9 <version_command><![CDATA[junction_saturation.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
11 @BAM_SAM_INPUTS@
15 junction_saturation.py 12 junction_saturation.py
16 --input-file '${input}' 13 --input-file 'input.${extension}'
17 --refgene '${refgene}' 14 --refgene '${refgene}'
18 --out-prefix output 15 --out-prefix output
19 --min-intron ${min_intron} 16 --min-intron ${min_intron}
20 --min-coverage ${min_coverage} 17 --min-coverage ${min_coverage}
21 --mapq ${mapq} 18 --mapq ${mapq}
53 </conditional> 50 </conditional>
54 <expand macro="rscript_output_param" /> 51 <expand macro="rscript_output_param" />
55 </inputs> 52 </inputs>
56 53
57 <outputs> 54 <outputs>
58 <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" /> 55 <expand macro="pdf_output_data" filename="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string}: junction saturation (PDF)"/>
59 <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" /> 56 <expand macro="rscript_output_data" filename="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string}: junction saturation (Rscript)"/>
60 </outputs> 57 </outputs>
61 58
62 <tests> 59 <tests>
63 <test> 60 <test>
64 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" /> 61 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />