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comparison pipe-t.xml @ 30:30ab487171ab draft

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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 488b3c091e8bf80f741a3e46b929427f1658ba3a-dirty
author davidecangelosi
date Thu, 10 Oct 2019 04:24:43 -0400
parents 7fbfe6f424f0
children e4281dad3291
comparison
equal deleted inserted replaced
29:8cb95051067d 30:30ab487171ab
1 <?xml version="1.0"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="pipe-t" name="PIPE-T" version="1.0" hidden="false"> 2 <tool id="pipe-t" name="PIPE-T" version="1.0" hidden="false">
3 <description>A tool for analyzing RTqPCR expression data </description> 3 <description>A tool for analyzing RTqPCR expression data</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.5.0">r-base</requirement> 5 <requirement type="package" version="3.5">r-base</requirement>
6 <requirement type="package" version="7.2.0">libgcc</requirement> 6 <requirement type="package" version="1.36.0">bioconductor-htqpcr</requirement>
7 <requirement type="package" version="1.36.0">bioconductor-htqpcr</requirement> 7 <requirement type="package" version="3.8.0">bioconductor-rankprod</requirement>
8 <requirement type="package" version="3.8.0">bioconductor-rankprod</requirement> 8 <requirement type="package" version="1.56.0">bioconductor-impute</requirement>
9 <requirement type="package" version="1.56.0">bioconductor-impute</requirement> 9 <requirement type="package" version="1.11.0">r-bbmisc</requirement>
10 <requirement type="package" version="1.11.0">r-bbmisc</requirement> 10 <requirement type="package" version="1.8.4">r-psych</requirement>
11 <requirement type="package" version="1.8.4">r-psych</requirement> 11 <requirement type="package" version="1.8_3">r-zoo</requirement>
12 <requirement type="package" version="1.8_3">r-zoo</requirement> 12 <requirement type="package" version="1.28.0">bioconductor-normqpcr</requirement>
13 <requirement type="package" version="1.28.0">bioconductor-normqpcr </requirement> 13 </requirements>
14 </requirements> 14 <command detect_errors="exit_code"><![CDATA[#for $input in $dp.list_files
15 <stdio> 15 ln -sf '$input' '$__tool_directory__/Symlink/${input.element_identifier}'&&
16 <exit_code range="1:" />
17 </stdio>
18 <command>
19 <![CDATA[
20 #for $input in $dp.list_files
21 ln -sf '$input' '$__tool_directory__/Symlink/${input.element_identifier}';
22 #end for 16 #end for
23 17
24 #if str( $dn.condNorm.normMethod ) == "deltaCt": 18 #if str( $dn.condNorm.normMethod ) == 'deltaCt':
25 #if str( $dn.condNorm.deltamethod.format ) == "userdefined": 19 #if str( $dn.condNorm.deltamethod.format ) == 'userdefined':
26 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": 20 #if str( $df.condImpute.format ) == 'mestdagh' or str( $df.condImpute.format ) == 'mean' or str( $df.condImpute.format ) == 'median' or str( $df.condImpute.format ) == 'cubic':
27 #if str( $de.condDEA.method ) == "ttest": 21 #if str( $de.condDEA.method ) == 'ttest':
28 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 22 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
29 #end if 23 #end if
30 #if str( $de.condDEA.method ) == "wtest": 24 #if str( $de.condDEA.method ) == 'wtest':
31 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 25 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
32 #end if 26 #end if
33 #if str( $de.condDEA.method ) == "rp": 27 #if str( $de.condDEA.method ) == 'rp':
34 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 28 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
35 #end if 29 #end if
36 #if str( $de.condDEA.method ) == "none": 30 #if str( $de.condDEA.method ) == 'none':
37 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 31 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
38 #end if 32 #end if
39 #end if 33 #end if
40 34
41 #if str( $df.condImpute.format ) == "knn": 35 #if str( $df.condImpute.format ) == 'knn':
42 #if str( $de.condDEA.method ) == "ttest": 36 #if str( $de.condDEA.method ) == 'ttest':
43 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 37 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
44 #end if 38 #end if
45 #if str( $de.condDEA.method ) == "wtest": 39 #if str( $de.condDEA.method ) == 'wtest':
46 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 40 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
47 #end if 41 #end if
48 #if str( $de.condDEA.method ) == "rp": 42 #if str( $de.condDEA.method ) == 'rp':
49 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 43 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
50 #end if 44 #end if
51 #if str( $de.condDEA.method ) == "none": 45 #if str( $de.condDEA.method ) == 'none':
52 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 46 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' '$dn.condNorm.deltamethod.normalizers' $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
53 #end if 47 #end if
54 #end if 48 #end if
55 #end if 49 #end if
56 #if str( $dn.condNorm.deltamethod.format ) == "genorm": 50 #if str( $dn.condNorm.deltamethod.format ) == 'genorm':
57 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": 51 #if str( $df.condImpute.format ) == 'mestdagh' or str( $df.condImpute.format ) == 'mean' or str( $df.condImpute.format ) == 'median' or str( $df.condImpute.format ) == 'cubic':
58 #if str( $de.condDEA.method ) == "ttest": 52 #if str( $de.condDEA.method ) == 'ttest':
59 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 53 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
60 #end if 54 #end if
61 #if str( $de.condDEA.method ) == "wtest": 55 #if str( $de.condDEA.method ) == 'wtest':
62 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 56 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
63 #end if 57 #end if
64 #if str( $de.condDEA.method ) == "rp": 58 #if str( $de.condDEA.method ) == 'rp':
65 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 59 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
66 #end if 60 #end if
67 #if str( $de.condDEA.method ) == "none": 61 #if str( $de.condDEA.method ) == 'none':
68 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 62 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
69 #end if 63 #end if
70 #end if 64 #end if
71 65
72 #if str( $df.condImpute.format ) == "knn": 66 #if str( $df.condImpute.format ) == 'knn':
73 #if str( $de.condDEA.method ) == "ttest": 67 #if str( $de.condDEA.method ) == 'ttest':
74 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 68 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
75 #end if 69 #end if
76 #if str( $de.condDEA.method ) == "wtest": 70 #if str( $de.condDEA.method ) == 'wtest':
77 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 71 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
78 #end if 72 #end if
79 #if str( $de.condDEA.method ) == "rp": 73 #if str( $de.condDEA.method ) == 'rp':
80 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 74 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
81 #end if 75 #end if
82 #if str( $de.condDEA.method ) == "none": 76 #if str( $de.condDEA.method ) == 'none':
83 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 77 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
84 #end if 78 #end if
85 #end if 79 #end if
86 #end if 80 #end if
87 #if str( $dn.condNorm.deltamethod.format ) == "normfinder": 81 #if str( $dn.condNorm.deltamethod.format ) == 'normfinder':
88 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": 82 #if str( $df.condImpute.format ) == 'mestdagh' or str( $df.condImpute.format ) == 'mean' or str( $df.condImpute.format ) == 'median' or str( $df.condImpute.format ) == 'cubic':
89 #if str( $de.condDEA.method ) == "ttest": 83 #if str( $de.condDEA.method ) == 'ttest':
90 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 84 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
91 #end if 85 #end if
92 #if str( $de.condDEA.method ) == "wtest": 86 #if str( $de.condDEA.method ) == 'wtest':
93 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 87 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
94 #end if 88 #end if
95 #if str( $de.condDEA.method ) == "rp": 89 #if str( $de.condDEA.method ) == 'rp':
96 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 90 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
97 #end if 91 #end if
98 #if str( $de.condDEA.method ) == "none": 92 #if str( $de.condDEA.method ) == 'none':
99 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 93 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
100 #end if 94 #end if
101 #end if 95 #end if
102 96
103 #if str( $df.condImpute.format ) == "knn": 97 #if str( $df.condImpute.format ) == 'knn':
104 #if str( $de.condDEA.method ) == "ttest": 98 #if str( $de.condDEA.method ) == 'ttest':
105 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 99 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
106 #end if 100 #end if
107 #if str( $de.condDEA.method ) == "wtest": 101 #if str( $de.condDEA.method ) == 'wtest':
108 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 102 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
109 #end if 103 #end if
110 #if str( $de.condDEA.method ) == "rp": 104 #if str( $de.condDEA.method ) == 'rp':
111 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 105 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
112 #end if 106 #end if
113 #if str( $de.condDEA.method ) == "none": 107 #if str( $de.condDEA.method ) == 'none':
114 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 108 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod '$dn.condNorm.deltamethod.format' $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
115 #end if 109 #end if
116 #end if 110 #end if
117 #end if 111 #end if
118 112
119 #else 113 #else
120 #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic": 114 #if str( $df.condImpute.format ) == 'mestdagh' or str( $df.condImpute.format ) == 'mean' or str( $df.condImpute.format ) == 'median' or str( $df.condImpute.format ) == 'cubic':
121 #if str( $de.condDEA.method ) == "ttest": 115 #if str( $de.condDEA.method ) == 'ttest':
122 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 116 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
123 #end if 117 #end if
124 #if str( $de.condDEA.method ) == "wtest": 118 #if str( $de.condDEA.method ) == 'wtest':
125 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 119 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
126 #end if 120 #end if
127 #if str( $de.condDEA.method ) == "rp": 121 #if str( $de.condDEA.method ) == 'rp':
128 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 122 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
129 #end if 123 #end if
130 #if str( $de.condDEA.method ) == "none": 124 #if str( $de.condDEA.method ) == 'none':
131 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 125 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
132 #end if 126 #end if
133 #end if 127 #end if
134 128
135 #if str( $df.condImpute.format ) == "knn": 129 #if str( $df.condImpute.format ) == 'knn':
136 #if str( $de.condDEA.method ) == "ttest": 130 #if str( $de.condDEA.method ) == 'ttest':
137 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 131 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
138 #end if 132 #end if
139 #if str( $de.condDEA.method ) == "wtest": 133 #if str( $de.condDEA.method ) == 'wtest':
140 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname"; 134 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 '$df.filtname';
141 #end if 135 #end if
142 #if str( $de.condDEA.method ) == "rp": 136 #if str( $de.condDEA.method ) == 'rp':
143 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 137 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
144 #end if 138 #end if
145 #if str( $de.condDEA.method ) == "none": 139 #if str( $de.condDEA.method ) == 'none':
146 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname"; 140 Rscript $__tool_directory__/pipe-t.R $dp.files '$dp.formatFile' $dp.n $galaxy_output1 '$__tool_directory__/Symlink' $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 '$df.filtname';
147 #end if 141 #end if
148 #end if 142 #end if
149 #end if 143 #end if]]></command>
150 ]]> 144 <inputs>
151 </command> 145 <section name="dp" title="File uploading and parsing" expanded="true">
152 <inputs> 146 <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list from the history tab" help="Collection should be of category List. " />
153 <section name="dp" title="File uploading and parsing" expanded="true"> 147 <param name="files" type="data" format="txt" label="Select one of the files from the history tab" help="File should contains only the columns: sampleName and Treatment." />
154 <param name="list_files" type="data_collection" collection_type="list" value="" label="Select a collection list from the history tab" help="Collection should be of category List. "/> 148 <param name="formatFile" type="select" label="Select one of the file formats from the list below." help="">
155 <param name="files" type="data" format="txt" label="Select one of the files from the history tab" help="File should contains only the columns: sampleName and Treatment." /> 149 <option value="EDS" selected="true">EDS</option>
156 <param name="formatFile" type="select" label="Select one of the file formats from the list below." help=""> 150 <option value="SDS">SDS</option>
157 <option value="EDS" selected="true">EDS</option> 151 <option value="OpenArray">OpenArray</option>
158 <option value="SDS" >SDS</option> 152 <option value="LightCycler">LightCycler</option>
159 <option value="OpenArray" >OpenArray</option> 153 <option value="CFX">CFX</option>
160 <option value="LightCycler" >LightCycler</option> 154 <option value="BioMark">BioMark</option>
161 <option value="CFX">CFX</option> 155 <option value="plain">Plain</option>
162 <option value="BioMark" >BioMark</option> 156 </param>
163 <option value="plain">Plain</option> 157 <param name="n" type="integer" min="1" max="1000" value="384" label="Type the number of transcripts in your file" />
164 </param> 158 </section>
165 <param name="n" type="integer" min="1" max="1000" value="384" label="Type the number of transcripts in your file" /> 159 <section name="dc" title="Ct filtering and categorization" expanded="true">
166 </section> 160 <param name="Ctmin" type="integer" min="0" max="40" value="14" label="Set up a minimum Ct value" help="Any Ct below your selected value will be labelled as Unreliable." />
167 <section name="dc" title="Ct filtering and categorization" expanded="true"> 161 <param name="Ctmax" type="integer" min="0" max="40" value="32" label="Set up a maximum Ct value" help="Any Ct above your selected value will be labelled as Unreliable." />
168 <param name="Ctmin" type="integer" min="0" max="40" value="14" label="Set up a minimum Ct value" 162 <param name="flag" type="select" label="Select TRUE if you want that PIPE-T assigns category 'Unreliable' on the basis of FAILURE flag" help="Data in qPCRset objects will have feature categories (Unreliable, Undetermined) assigned to them based on different Ct criteria.">
169 help="Any Ct below your selected value will be labelled as Unreliable." /> 163 <option value="TRUE">TRUE</option>
170 <param name="Ctmax" type="integer" min="0" max="40" value="32" label="Set up a maximum Ct value" 164 <option value="FALSE">FALSE</option>
171 help="Any Ct above your selected value will be labelled as Unreliable."/> 165 </param>
172 <param name="flag" type="select" label="Select TRUE if you want that PIPE-T assigns category 'Unreliable' on the basis of FAILURE flag" help="Data in qPCRset objects will have feature categories (Unreliable, Undetermined) assigned to them based on different Ct criteria."> 166 </section>
173 <option value="TRUE">TRUE</option> 167 <section name="dn" title="Normalization" expanded="true">
174 <option value="FALSE">FALSE</option> 168 <conditional name="condNorm">
175 </param> 169 <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability in the data.">
176 </section> 170 <option value="globalmean" selected="true">Global mean</option>
177 <section name="dn" title="Normalization" expanded="true"> 171 <option value="deltaCt">DeltaCt method (housekeeping genes)</option>
178 <conditional name="condNorm"> 172 <option value="geometric.mean">Modified global mean</option>
179 <param name="normMethod" type="select" label="Select one of the normalization methods from the list below." help="Normalization is important to reduce technical variability in the data."> 173 <option value="quantile">Quantile</option>
180 <option value="globalmean" selected="true">Global mean</option> 174 <option value="norm.rankinvariant">Rank invariant</option>
181 <option value="deltaCt">DeltaCt method (housekeeping genes)</option> 175 <option value="scale.rankinvariant">Scale rank invariant</option>
182 <option value="geometric.mean">Modified global mean</option> 176 </param>
183 <option value="quantile">Quantile</option> 177 <when value="deltaCt">
184 <option value="norm.rankinvariant">Rank invariant</option> 178 <conditional name="deltamethod">
185 <option value="scale.rankinvariant">Scale rank invariant</option> 179 <param name="format" type="select" label="Select one of the methods from the list below for selecting normalizers." help="">
186 </param> 180 <option value="userdefined" selected="true">User defined</option>
187 <when value="deltaCt"> 181 <option value="genorm">geNorm</option>
188 <conditional name="deltamethod"> 182 <option value="normfinder">NormFinder</option>
189 <param name="format" type="select" label="Select one of the methods from the list below for selecting normalizers." help=""> 183 </param>
190 <option value="userdefined" selected="true">User defined</option> 184 <when value="userdefined">
191 <option value="genorm">geNorm</option> 185 <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcripts that will be used as normalizers." value="U6 snRNA-001973" />
192 <option value="normfinder">NormFinder</option> 186 </when>
193 </param> 187 <when value="genorm">
194 <when value="userdefined"> 188 <param name="minhkgenorm" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by geNorm method." value="2" />
195 <param name="normalizers" type="text" label="Type a comma separated list of housekeeping transcripts that will be used as normalizers." value="U6 snRNA-001973"></param> 189 </when>
196 </when> 190 <when value="normfinder">
197 <when value="genorm"> 191 <param name="minhknormfinder" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by NormFinder method." value="1" />
198 <param name="minhkgenorm" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by geNorm method." value="2"></param> 192 </when>
199 </when> 193 </conditional>
200 <when value="normfinder"> 194 </when>
201 <param name="minhknormfinder" type="integer" label="Type the minimum number of housekeeping transcripts that will be considered by NormFinder method." value="1"></param> 195 </conditional>
202 </when> 196 </section>
203 </conditional> 197 <section name="df" title="Transcript filtering and imputation" expanded="true">
204 </when> 198 <param name="percent" type="integer" min="0" max="100" value="0" label="Set up a percentage of NAs." help="Transcripts with more than the specified percentage of NAs across all samples will be removed." />
205 </conditional> 199 <param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="Transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a" />
206 </section> 200 <conditional name="condImpute">
207 <section name="df" title="Transcript filtering and imputation" expanded="true"> 201 <param name="format" type="select" label="Select one of the imputation methods from the list below." help="">
208 <param name="percent" type="integer" min="0" max="100" value="0" label="Set up a percentage of NAs." 202 <option value="mestdagh" selected="true">Mestdagh</option>
209 help="Transcripts with more than the specified percentage of NAs across all samples will be removed." /> 203 <option value="knn">K-Nearest Neighbour</option>
210 <param name="filtname" type="text" label="Type a comma separeted list of transcript identifiers to filter out" help="Transcript identifiers specified in the List will be removed." value="U6 snRNA-001973,hsa-miR-520a"> 204 <option value="cubic">Cubic Spline</option>
211 </param> 205 </param>
212 <conditional name="condImpute"> 206 <when value="knn">
213 <param name="format" type="select" label="Select one of the imputation methods from the list below." help=""> 207 <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use in the KNN imputation method" />
214 <option value="mestdagh" selected="true">Mestdagh</option> 208 <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcripts to use in the KNN method." help="Larger numbers are divided by two-means clustering (recursively) prior to imputation. " />
215 <option value="knn">K-Nearest Neighbour</option> 209 </when>
216 <option value="cubic">Cubic Spline</option> 210 </conditional>
217 </param> 211 </section>
218 <when value="knn"> 212 <section name="de" title="Differential expression analysis" expanded="true">
219 <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use in the KNN imputation method" /> 213 <conditional name="condDEA">
220 <param name="maxp" type="integer" min="1" max="2000" value="1500" label="Type the maximum number of imputed transcripts to use in the KNN method." help="Larger numbers are divided by two-means clustering (recursively) 214 <param name="method" type="select" label="Select one of the methods from the list below or NONE.">
221 prior to imputation. "/> 215 <option value="ttest" selected="true">T-test and fold change</option>
222 </when> 216 <option value="wtest" selected="true">Two sample Wilcoxon test and fold change</option>
223 </conditional> 217 <option value="rp">Rank Product (Only for unpaired data)</option>
224 </section> 218 <option value="none">NONE</option>
225 <section name="de" title="Differential expression analysis" expanded="true"> 219 </param>
226 <conditional name="condDEA"> 220 <when value="ttest">
227 <param name="method" type="select" label="Select one of the methods from the list below or NONE."> 221 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance.">
228 222 <option value="two.sided" selected="true">Two sided</option>
229 <option value="ttest" selected="true">T-test and fold change</option> 223 <option value="greater">Greater</option>
230 <option value="wtest" selected="true"> Two sample Wilcoxon test and fold change</option> 224 <option value="less">Lower</option>
231 <option value="rp">Rank Product (Only for unpaired data)</option> 225 </param>
232 <option value="none">NONE</option> 226 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file">
233 </param> 227 <option value="TRUE">TRUE</option>
234 <when value="ttest"> 228 <option value="FALSE" selected="true">FALSE</option>
235 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance."> 229 </param>
236 <option value="two.sided" selected="true">Two sided</option> 230 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately.">
237 <option value="greater">Greater</option> 231 <option value="TRUE" selected="true">TRUE</option>
238 <option value="less">Lower</option> 232 <option value="FALSE">FALSE</option>
239 </param> 233 </param>
240 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file"> 234 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help="">
241 <option value="TRUE" >TRUE</option> 235 <option value="TRUE" selected="true">TRUE</option>
242 <option value="FALSE" selected="true">FALSE</option> 236 <option value="FALSE">FALSE</option>
243 </param> 237 </param>
244 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately."> 238 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined.">
245 <option value="TRUE" selected="true">TRUE</option> 239 <option value="TRUE" selected="true">TRUE</option>
246 <option value="FALSE" >FALSE</option> 240 <option value="FALSE">FALSE</option>
247 </param> 241 </param>
248 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help=""> 242 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing">
249 <option value="TRUE" selected="true">TRUE</option> 243 <option value="BH" selected="true">Benjamini-Hochberg</option>
250 <option value="FALSE" >FALSE</option> 244 <option value="bonferroni">Bonferroni</option>
251 </param> 245 </param>
252 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and 246 </when>
253 biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined."> 247 <when value="wtest">
254 <option value="TRUE" selected="true">TRUE</option> 248 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance.">
255 <option value="FALSE" >FALSE</option> 249 <option value="two.sided" selected="true">Two sided</option>
256 </param> 250 <option value="greater">Greater</option>
257 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing"> 251 <option value="less">Lower</option>
258 <option value="BH" selected="true">Benjamini-Hochberg</option> 252 </param>
259 <option value="bonferroni">Bonferroni</option> 253 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file">
260 </param> 254 <option value="TRUE">TRUE</option>
261 </when> 255 <option value="FALSE" selected="true">FALSE</option>
262 <when value="wtest"> 256 </param>
263 <param name="alternative" type="select" label="Select one of the types of alternative hypothesis to assess significance."> 257 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately.">
264 <option value="two.sided" selected="true">Two sided</option> 258 <option value="TRUE" selected="true">TRUE</option>
265 <option value="greater">Greater</option> 259 <option value="FALSE">FALSE</option>
266 <option value="less">Lower</option> 260 </param>
267 </param> 261 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help="">
268 <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file"> 262 <option value="TRUE" selected="true">TRUE</option>
269 <option value="TRUE" >TRUE</option> 263 <option value="FALSE">FALSE</option>
270 <option value="FALSE" selected="true">FALSE</option> 264 </param>
271 </param> 265 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined.">
272 <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately."> 266 <option value="TRUE" selected="true">TRUE</option>
273 <option value="TRUE" selected="true">TRUE</option> 267 <option value="FALSE">FALSE</option>
274 <option value="FALSE" >FALSE</option> 268 </param>
275 </param> 269 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing">
276 <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help=""> 270 <option value="BH" selected="true">Benjamini-Hochberg</option>
277 <option value="TRUE" selected="true">TRUE</option> 271 <option value="bonferroni">Bonferroni</option>
278 <option value="FALSE" >FALSE</option> 272 </param>
279 </param> 273 </when>
280 <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and 274 <when value="rp" />
281 biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined."> 275 </conditional>
282 <option value="TRUE" selected="true">TRUE</option> 276 </section>
283 <option value="FALSE" >FALSE</option> 277 </inputs>
284 </param> 278 <outputs>
285 <param name="padjust" type="select" label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing"> 279 <data format="txt" name="galaxy_output1" label="1_Ct_Raw" />
286 <option value="BH" selected="true">Benjamini-Hochberg</option> 280 <data format="png" name="galaxy_output2" label="2_Boxplot after data categorization" />
287 <option value="bonferroni">Bonferroni</option> 281 <data format="txt" name="galaxy_output3" label="3_Normalized data" />
288 </param> 282 <data format="png" name="galaxy_output4" label="4_ECDF" />
289 </when> 283 <data format="png" name="galaxy_output6" label="5_Boxplot after data normalization" />
290 <when value="rp"> 284 <data format="txt" name="galaxy_output5" label="6_Imputed data" />
291 </when> 285 <data format="txt" name="galaxy_output7" label="7_Differentially Expressed transcripts" />
292 </conditional> 286 </outputs>
293 </section> 287 <tests>
294 </inputs> 288 <test>
295 <outputs> 289 <section name="dp">
296 <data format="txt" name="galaxy_output1" label="1_Ct_Raw"/> 290 <param name="list_files">
297 <data format="png" name="galaxy_output2" label="2_Boxplot after data categorization"/> 291 <collection type="list">
298 <data format="txt" name="galaxy_output3" label="3_Normalized data"/> 292 <element name="GSM628070_18b.txt" value="GSM628070_18b.txt" />
299 <data format="png" name="galaxy_output4" label="4_ECDF"/> 293 <element name="GSM628068_15b.txt" value="GSM628068_15b.txt" />
300 <data format="png" name="galaxy_output6" label="5_Boxplot after data normalization"/> 294 <element name="GSM628072_202b.txt" value="GSM628072_202b.txt" />
301 <data format="txt" name="galaxy_output5" label="6_Imputed data"/> 295 <element name="GSM628080_22b.txt" value="GSM628080_22b.txt" />
302 <data format="txt" name="galaxy_output7" label="7_Differentially Expressed transcripts"/> 296 <element name="GSM628084_236b.txt" value="GSM628084_236b.txt" />
303 </outputs> 297 <element name="GSM628085_23b.txt" value="GSM628085_23b.txt" />
304 298 <element name="GSM628090_31b.txt" value="GSM628090_31b.txt" />
305 <help> 299 <element name="GSM628093_49b1.txt" value="GSM628093_49b1.txt" />
306 <![CDATA[ 300 <element name="GSM628094_49b2.txt" value="GSM628094_49b2.txt" />
307 **What it does** 301 <element name="GSM628101_5b.txt" value="GSM628101_5b.txt" />
302 <element name="GSM628073_204b.txt" value="GSM628073_204b.txt" />
303 <element name="GSM628096_4b.txt" value="GSM628096_4b.txt" />
304 <element name="GSM628100_59b.txt" value="GSM628100_59b.txt" />
305 <element name="GSM628104_6b1.txt" value="GSM628104_6b1.txt" />
306 <element name="GSM628105_6b2.txt" value="GSM628105_6b2.txt" />
307 <element name="GSM628106_7b.txt" value="GSM628106_7b.txt" />
308 </collection>
309 </param>
310 <param name="files" value="List_OLIGOvsPOLY_Metastatic.txt" />
311 <param name="formatFile" value="SDS" />
312 <param name="n" value="191" />
313 </section>
314 <section name="dc">
315 <param name="Ctmin" value="14" />
316 <param name="Ctmax" value="32" />
317 <param name="flag" value="FALSE" />
318 </section>
319 <section name="dn">
320 <param name="normMethod" value="deltaCt" />
321 <param name="format" value="genorm" />
322 <param name="minhkgenorm" value="2" />
323 </section>
324 <section name="df">
325 <param name="percent" value="10" />
326 <param name="filtname" value="Empty." />
327 <param name="format" value="cubic" />
328 </section>
329 <section name="de">
330 <param name="method" value="rp" />
331 </section>
332 <output name="galaxy_output1" file="Output_Ct_Raw.txt" />
333 <output name="galaxy_output2" file="Output_Boxplot_after_data_categorization.png" />
334 <output name="galaxy_output3" file="Output_Normalized_data.txt" />
335 <output name="galaxy_output4" file="Output_ECDF.png" />
336 <output name="galaxy_output6" file="Output_Boxplot_after_data_normalization.png" />
337 <output name="galaxy_output5" file="Output_Imputed_data.txt" />
338 <output name="galaxy_output7" file="Output_Differentially_Expressed_transcripts.txt" />
339 </test>
340 </tests>
341 <help><![CDATA[**What it does**
308 INPUTS: This tool parses a list of RT-qPCR file and a file associating these files and one of two groups 342 INPUTS: This tool parses a list of RT-qPCR file and a file associating these files and one of two groups
309 OUTPUTS: and returs 343 OUTPUTS: and returs
310 1) A txt file with the raw Ct data 344 1) A txt file with the raw Ct data
311 2) A PNG file of a boxplot with the Ct data after data categorization for each sample 345 2) A PNG file of a boxplot with the Ct data after data categorization for each sample
312 3) A txt file with normalized data 346 3) A txt file with normalized data
313 4) A PNG file with the Empirical cumulative distribution before and after data normalization 347 4) A PNG file with the Empirical cumulative distribution before and after data normalization
314 5) A PNG file of a boxplot with the normalzied data for each sample 348 5) A PNG file of a boxplot with the normalzied data for each sample
315 6) A txt file with imputed data for each missing value 349 6) A txt file with imputed data for each missing value
316 7) A txt file with the results of the differntial expression analyis 350 7) A txt file with the results of the differntial expression analyis]]></help>
317 ]]>
318 </help>
319 </tool> 351 </tool>