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comparison FPKM_count.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_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"/> 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>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 11
12 <version_command><![CDATA[FPKM_count.py --version]]></version_command> 12 <version_command><![CDATA[FPKM_count.py --version]]></version_command>
13 13
14 <command><![CDATA[ 14 <command><![CDATA[
15 ln -sf '${input}' 'local_input.bam' && 15 @BAM_SAM_INPUTS@
16 ln -sf '${input.metadata.bam_index}' 'local_input.bam.bai' && 16 FPKM_count.py -i 'input.${extension}' -o output -r '${refgene}'
17 FPKM_count.py -i 'local_input.bam' -o output -r '${refgene}'
18 17
19 #if str($strand_type.strand_specific) == "pair" 18 #if str($strand_type.strand_specific) == "pair"
20 -d 19 -d
21 #if str($strand_type.pair_type) == "sd" 20 #if str($strand_type.pair_type) == "sd"
22 '1++,1--,2+-,2-+' 21 '1++,1--,2+-,2-+'