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comparison RPKM_saturation.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
comparison
equal deleted inserted replaced
62:473382134e56 63:27e16a30667a
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 <macros> 3 <macros>
4 <import>rseqc_macros.xml</import> 4 <import>rseqc_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 7 <expand macro="requirements"/>
8 <expand macro="requirements" /> 8 <expand macro="stdio"/>
9
10 <expand macro="stdio" />
11
12 <version_command><![CDATA[RPKM_saturation.py --version]]></version_command> 9 <version_command><![CDATA[RPKM_saturation.py --version]]></version_command>
13
14 <command><![CDATA[ 10 <command><![CDATA[
15 @BAM_SAM_INPUTS@ 11 @BAM_SAM_INPUTS@
16 RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}' 12 RPKM_saturation.py -i 'input.${extension}' -o output -r '${refgene}'
17 13
18 #if str($strand_type.strand_specific) == "pair" 14 #if str($strand_type.strand_specific) == "pair"
34 #end if 30 #end if
35 31
36 -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff} 32 -l ${percentileFloor} -u ${percentileCeiling} -s ${percentileStep} -c ${rpkmCutoff}
37 --mapq $mapq 33 --mapq $mapq
38 ]]></command> 34 ]]></command>
39
40 <inputs> 35 <inputs>
41 <expand macro="bam_sam_param" /> 36 <expand macro="bam_sam_param"/>
42 <expand macro="refgene_param" /> 37 <expand macro="refgene_param"/>
43 <expand macro="strand_type_param" /> 38 <expand macro="strand_type_param"/>
44 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/> 39 <param name="percentileFloor" type="integer" value="5" label="Begin sampling from this percentile (default=5)" help="(--percentile-floor)"/>
45 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)" /> 40 <param name="percentileCeiling" type="integer" value="100" label="End sampling at this percentile (default=100)" help="(--percentile-ceiling)"/>
46 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)" /> 41 <param name="percentileStep" type="integer" value="5" label="Sampling step size (default=5)" help="(--percentile-step)"/>
47 <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)" /> 42 <param name="rpkmCutoff" type="text" value="0.01" label="Ignore transcripts with RPKM smaller than this number (default=0.01)" help="(--rpkm-cutoff)"/>
48 <expand macro="mapq_param" /> 43 <expand macro="mapq_param"/>
49 <expand macro="rscript_output_param" /> 44 <expand macro="rscript_output_param"/>
50 </inputs> 45 </inputs>
51
52 <outputs> 46 <outputs>
53 <expand macro="pdf_output_data" filename="output.saturation.pdf" /> 47 <expand macro="pdf_output_data" filename="output.saturation.pdf"/>
54 <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/> 48 <data format="tabular" name="outputxls" from_work_dir="output.eRPKM.xls" label="${tool.name} on ${on_string}: RPKM"/>
55 <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/> 49 <data format="tabular" name="outputrawxls" from_work_dir="output.rawCount.xls" label="${tool.name} on ${on_string}: raw count"/>
56 <expand macro="rscript_output_data" filename="output.saturation.r" /> 50 <expand macro="rscript_output_data" filename="output.saturation.r"/>
57 </outputs> 51 </outputs>
58
59 <tests> 52 <tests>
60 <test> 53 <test expect_num_outputs="4">
61 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/> 54 <param name="input" value="pairend_strandspecific_51mer_hg19_random.bam"/>
62 <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/> 55 <param name="refgene" value="hg19.HouseKeepingGenes_30.bed"/>
63 <param name="rscript_output" value="true" /> 56 <param name="rscript_output" value="true"/>
64 <output name="outputxls"> 57 <output name="outputxls">
65 <assert_contents> 58 <assert_contents>
66 <has_n_columns n="26" /> 59 <has_n_columns n="26"/>
67 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> 60 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/>
68 </assert_contents> 61 </assert_contents>
69 </output> 62 </output>
70 <output name="outputrawxls"> 63 <output name="outputrawxls">
71 <assert_contents> 64 <assert_contents>
72 <has_n_columns n="26" /> 65 <has_n_columns n="26"/>
73 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*" /> 66 <has_line_matching expression="chr1\t16174358\t16266950\tNM_015001.*"/>
74 </assert_contents> 67 </assert_contents>
75 </output> 68 </output>
76 <output name="outputr"> 69 <output name="outputr">
77 <assert_contents> 70 <assert_contents>
78 <has_text text="pdf('output.saturation.pdf')" /> 71 <has_text text="pdf('output.saturation.pdf')"/>
79 <has_line_matching expression="S5=c\(\d+\.\d+\)" /> 72 <has_line_matching expression="S5=c\(\d+\.\d+\)"/>
80 </assert_contents> 73 </assert_contents>
81 </output> 74 </output>
82 <output name="outputpdf" file="output.saturation.pdf" compare="sim_size" /> 75 <output name="outputpdf" file="output.saturation.pdf" compare="sim_size"/>
83 </test> 76 </test>
84 </tests> 77 </tests>
85
86 <help><![CDATA[ 78 <help><![CDATA[
87 RPKM_saturation.py 79 RPKM_saturation.py
88 ++++++++++++++++++ 80 ++++++++++++++++++
89 81
90 The precision of any sample statitics (RPKM) is affected by sample size (sequencing depth); 82 The precision of any sample statitics (RPKM) is affected by sample size (sequencing depth);
161 153
162 @ABOUT@ 154 @ABOUT@
163 155
164 ]]> 156 ]]>
165 </help> 157 </help>
166 158 <expand macro="citations"/>
167 <expand macro="citations" />
168
169 </tool> 159 </tool>