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comparison FPKM_count.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 b21f0167e197
comparison
equal deleted inserted replaced
12:57fad5deeb8e 13:a7f9084572fe
1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_FPKM_count" name="FPKM Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>calculates raw read count, FPM, and FPKM for each gene</description> 2 <description>calculates raw read count, FPM, and FPKM for each gene</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>
6
7 <expand macro="bio_tools"/>
7 8
8 <expand macro="requirements" /> 9 <expand macro="requirements" />
9 10
10 <expand macro="stdio" /> 11 <expand macro="stdio" />
11 12
12 <version_command><![CDATA[FPKM_count.py --version]]></version_command> 13 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
13 14
14 <command><![CDATA[ 15 <command><![CDATA[
15 ln -sf '${input}' 'local_input.bam' && 16 @BAM_SAM_INPUTS@
16 ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' && 17 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
17 FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
18 18
19 #if str($strand_type.strand_specific) == "pair" 19 #if str($strand_type.strand_specific) == "pair"
20 -d 20 -d
21 #if str($strand_type.pair_type) == "sd" 21 #if str($strand_type.pair_type) == "sd"
22 '1++,1--,2+-,2-+' 22 '1++,1--,2+-,2-+'