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comparison deseq2.xml @ 12:bd06df00180a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
author iuc
date Mon, 29 Jan 2018 07:30:18 -0500
parents 25204a860b79
children 3660c9088494
comparison
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11:25204a860b79 12:bd06df00180a
1 <tool id="deseq2" name="DESeq2" version="2.11.40"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.1">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> 4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> 5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
6 <requirement type="package" version="0.6.5">r-ggrepel</requirement>
7 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
6 </requirements> 8 </requirements>
7 <stdio> 9 <stdio>
8 <regex match="Execution halted" 10 <regex match="Execution halted"
9 source="both" 11 source="both"
10 level="fatal" 12 level="fatal"
29 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && 31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
30 #end if 32 #end if
31 #end if 33 #end if
32 34
33 #import json 35 #import json
36 #import os
34 Rscript '${__tool_directory__}/deseq2.R' 37 Rscript '${__tool_directory__}/deseq2.R'
35 -o '$deseq_out' 38 -o '$deseq_out'
36 #if $pdf: 39 #if $pdf:
37 -p '$plots' 40 -p '$plots'
38 #end if 41 #end if
39 #if $normCounts: 42 #if $normCounts:
40 -n '$counts_out' 43 -n '$counts_out'
41 #end if 44 #end if
45 #set $filename_to_element_identifiers = {}
42 #set $temp_factor_names = list() 46 #set $temp_factor_names = list()
43 #for $factor in $rep_factorName: 47 #for $factor in $rep_factorName:
44 #set $temp_factor = list() 48 #set $temp_factor = list()
45 #for $level in $factor.rep_factorLevel: 49 #for $level in $factor.rep_factorLevel:
46 #set $count_files = list() 50 #set $count_files = list()
47 #for $file in $level.countsFile: 51 #for $file in $level.countsFile:
48 $count_files.append(str($file)) 52 $count_files.append(str($file))
53 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
49 #end for 54 #end for
50 $temp_factor.append( {str($level.factorLevel): $count_files} ) 55 $temp_factor.append( {str($level.factorLevel): $count_files} )
51 #end for 56 #end for
52 $temp_factor.reverse() 57 $temp_factor.reverse()
53 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 58 $temp_factor_names.append([str($factor.factorName), $temp_factor])
54 #end for 59 #end for
55 -f '#echo json.dumps(temp_factor_names)#' 60 -f '#echo json.dumps(temp_factor_names)#'
61 -l '#echo json.dumps(filename_to_element_identifiers)#'
56 -t $fit_type 62 -t $fit_type
57 #if $outlier_replace_off: 63 #if $outlier_replace_off:
58 -a 64 -a
59 #end if 65 #end if
60 #if $outlier_filter_off: 66 #if $outlier_filter_off: