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comparison RPKM_saturation.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
comparison
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59:dbedfc5f5a3c 60:1421603cc95b
1 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@.2"> 1 <tool id="rseqc_RPKM_saturation" name="RPKM Saturation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</description> 2 <description>calculates raw count and RPKM values for transcript at exon, intron, and mRNA level</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[RPKM_saturation.py --version]]></version_command> 12 <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
13 13
14 <command><![CDATA[ 14 <command><![CDATA[
15 RPKM_saturation.py -i '${input}' -o output -r '${refgene}' 15 @BAM_SAM_INPUTS@
16 RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}'
16 17
17 #if str($strand_type.strand_specific) == "pair" 18 #if str($strand_type.strand_specific) == "pair"
18 -d 19 -d
19 #if str($strand_type.pair_type) == "sd" 20 #if str($strand_type.pair_type) == "sd"
20 '1++,1--,2+-,2-+' 21 '1++,1--,2+-,2-+'
35 -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff} 36 -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff}
36 --mapq $mapq 37 --mapq $mapq
37 ]]></command> 38 ]]></command>
38 39
39 <inputs> 40 <inputs>
40 <expand macro="bam_param" /> 41 <expand macro="bam_sam_param" />
41 <expand macro="refgene_param" /> 42 <expand macro="refgene_param" />
42 <expand macro="strand_type_param" /> 43 <expand macro="strand_type_param" />
43 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/> 44 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
44 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" /> 45 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" />
45 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" /> 46 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" />