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comparison deseq2_normalization.xml @ 3:71a9c73d989a draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization commit a4201d38a9ceba983fa0b800dff981bd3a626866
author artbio
date Thu, 07 Nov 2024 17:54:47 +0000
parents 8faa01102fbc
children
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2:8faa01102fbc 3:71a9c73d989a
1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.40.2+galaxy0" profile="22.01"> 1 <tool id="deseq2_normalization" name="DESeq2 normalization" version="1.40.2+galaxy1" profile="22.01">
2 <description>of hit lists (geometric method)</description> 2 <description>of hit lists (geometric method)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement> 4 <requirement type="package" version="1.40.2">bioconductor-deseq2</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Tool exception" /> 7 <exit_code range="1:" level="fatal" description="Tool exception" />
29 colnames(norm_table) = c("gene", colnames(countsTable)) 29 colnames(norm_table) = c("gene", colnames(countsTable))
30 write.table(norm_table, file = "${norm_hit_table}", row.names = FALSE, col.names = TRUE, 30 write.table(norm_table, file = "${norm_hit_table}", row.names = FALSE, col.names = TRUE,
31 quote = FALSE, dec = ".", sep = "\t", eol = "\n") 31 quote = FALSE, dec = ".", sep = "\t", eol = "\n")
32 </configfile> 32 </configfile>
33 </configfiles> 33 </configfiles>
34 <inputs> 34 <inputs>
35 <param name="input" type="data" format="tabular" label="Hit lists of items"/> 35 <param name="input" type="data" format="tabular" label="Hit lists of items"/>
36 </inputs> 36 </inputs>
37 <outputs> 37 <outputs>
38 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" /> 38 <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" />
39 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" /> 39 <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" />
40 </outputs> 40 </outputs>
41 <tests> 41 <tests>
42 <test> 42 <test>
43 <param name="input" value="counts.tab" ftype="tabular"/> 43 <param name="input" value="counts.tab" ftype="tabular"/>
44 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/> 44 <output name="output_factors" file="norm_factors.tab" ftype="tabular"/>
45 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/> 45 <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/>
104 NM_177834 1 3 2 0 104 NM_177834 1 3 2 0
105 105
106 NM_145381 606 445 367 306 106 NM_145381 606 445 367 306
107 107
108 ]]> 108 ]]>
109
110
111 </help> 109 </help>
112 <citations> 110 <citations>
113 <citation type="doi">10.1186/s13059-014-0550-8</citation> 111 <citation type="doi">10.1186/s13059-014-0550-8</citation>
114 </citations> 112 </citations>
115 </tool> 113 </tool>