Mercurial > repos > iuc > masigpro

annotate masigpro.xml @ 0:c8c290f3ea7d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
author iuc
date Mon, 15 May 2017 07:29:03 -0400
parents
children cc96abdef027
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
1 <tool id="masigpro" name="maSigPro" version="1.49.0.0">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
2 <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
3 <requirements>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
4 <requirement type="package" version="1.49.0">bioconductor-masigpro</requirement>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
5 <requirement type="package" version="1.3.2">r-optparse</requirement>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
6 <requirement type="package" version="4.4">sed</requirement>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
7 </requirements>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
8 <stdio>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
9 <regex match="Execution halted"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
10 source="both"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
11 level="fatal"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
12 description="Execution halted." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
13 <regex match="Error in"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
14 source="both"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
15 level="fatal"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
16 description="An undefined error occurred, please check your input carefully and contact your administrator." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
17 <regex match="Fatal error"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
18 source="both"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
19 level="fatal"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
20 description="An undefined error occurred, please check your input carefully and contact your administrator." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
21 </stdio>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
22 <version_command>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
23 <![CDATA[
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
24 echo $(R --version | grep version | grep -v GNU)", maSigPro version" $(R --vanilla --slave -e "library(maSigPro); cat(sessionInfo()\$otherPkgs\$maSigPro\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
25 ]]>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
26 </version_command>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
27 <command>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
28 <![CDATA[
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
29 #if str($source.source_selector) == "advanced":
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
30 paste
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
31 #set $start = True
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
32 #set $header = ''
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
33 #for $time in $source.rep_time:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
34 #for $file in $time.files:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
35 #if $start:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
36 <(cut -f1 $file)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
37 #set $start = False
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
38 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
39 #set $header += ' "' + $file.name + '"'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
40 <(cut -f2 $file)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
41 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
42 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
43 > data && sed -i '1i$header' data &&
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
44 #if $source.enable_output:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
45 ln -f data $data_out && ln -f $design_matrix $edesign_out &&
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
46 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
47 #set $data = 'data'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
48 #set $edesign = $design_matrix
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
49 #else:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
50 #set $data = $source.data
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
51 #set $edesign = $source.edesign
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
52 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
53 Rscript '${__tool_directory__}/masigpro.R'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
54 -e '$edesign'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
55 -d '$data'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
56 -o '$masigpro_out'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
57 #if str($source.source_selector) == "defaults":
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
58 --time_col $source.time_col
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
59 --repl_col $source.repl_col
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
60 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
61 --degree $makeDesignMatrix.degree
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
62 --qvalue $p_vector.qvalue
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
63 --min_obs $p_vector.min_obs
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
64 --step_method '$Tfit.step_method'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
65 --nvar_correction $Tfit.nvar_correction
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
66 --alfa $Tfit.alfa
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
67 --rsq $getSiggenes.rsq
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
68 --vars '$getSiggenes.vars'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
69 --significant_intercept '$getSiggenes.significant_intercept'
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
70 #if $pdf.pdf_selector:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
71 --cluster_data $pdf.seeGenes.clusterData
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
72 -k $pdf.seeGenes.k
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
73 --cluster_method $pdf.seeGenes.clustering.clusterMethod
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
74 #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust":
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
75 --distance $pdf.seeGenes.clustering.distance
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
76 --agglo_method $pdf.seeGenes.clustering.aggloMethod
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
77 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
78 #if str($pdf.seeGenes.clustering.clusterMethod) == "kmeans":
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
79 --iter_max $pdf.seeGenes.clustering.iterMax
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
80 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
81 --color_mode $pdf.seeGenes.colorMode
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
82 --show_fit $pdf.seeGenes.showFit
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
83 --show_lines $pdf.seeGenes.showLines
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
84 --cexlab $pdf.seeGenes.cexlab
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
85 --legend $pdf.seeGenes.legend
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
86 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
87 ]]>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
88 </command>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
89 <configfiles>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
90 <configfile name="design_matrix">#if str($source.source_selector) == "advanced":
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
91 #set $header = "Name Time Replicate"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
92 #for $group in $source.rep_groups:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
93 #set $header = $header + ' ' + str($group.name)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
94 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
95 $header
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
96 #set $c = len($source.rep_repl) + 1
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
97 #for $time in $source.rep_time:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
98 #for $file in $time.files:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
99 #set $is_repl = False
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
100 #for $i, $repl in enumerate($source.rep_repl):
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
101 #if str($file) in str($repl.files):
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
102 #set $r = $i + 1
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
103 #set $is_repl = True
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
104 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
105 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
106 #if $is_repl == False:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
107 #set $r = $c
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
108 #set $c += 1
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
109 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
110 #set $line = '"' + str($file.name) + '" ' + str($time.time) + ' ' + str($r)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
111 #for $group in $source.rep_groups:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
112 #if str($file) in str($group.files):
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
113 #set $line += " 1"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
114 #else
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
115 #set $line += " 0"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
116 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
117 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
118 $line
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
119 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
120 #end for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
121 #end if
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
122 </configfile>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
123 </configfiles>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
124 <inputs>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
125 <conditional name="source">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
126 <param label="Choose data source" name="source_selector"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
127 help="Choose if you want to provide seperate count files (e.g. from HTSeq-count or feature-seq)
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
128 and define your experiment design matrix here, or if you have maSigPro edesign and data input files already."
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
129 type="select">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
130 <option value="defaults">Use maSigPro edesign and data files</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
131 <option value="advanced">Seperate count data (e.g. from HTSeq-count or feature-count)</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
132 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
133 <when value="defaults">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
134 <param name="edesign" format="tabular,txt" type="data" label="Experiment matrix"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
135 help="Matrix describing experimental design. Rows must be arrays and columns experiment descriptors" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
136 <param name="data" format="tabular,txt" type="data" label="Gene expression matrix"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
137 help="Matrix containing normalized gene expression data. Genes must be in rows and arrays in columns" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
138 <param name="time_col" label="Column number containing time values" type="integer" value="1"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
139 help="Column number in edesign containing time values. Default is first column" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
140 <param name="repl_col" label="Column number containing replicate coding" type="integer" value="2"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
141 help="Column number in edesign containing coding for replicate arrays. Default is second column" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
142 </when>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
143 <when value="advanced">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
144 <param name="enable_output" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output generated maSigPro input files?"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
145 help="Choose if you want to output the generated edesign and data files for direct use in maSigPro as history elements." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
146 <repeat name="rep_time" title="Time values" min="1" default="1">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
147 <param name="time" type="integer" value="0" label="Specify a numerical time value" help="Only numbers will be allowed">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
148 <sanitizer>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
149 <valid initial="string.digits"></valid>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
150 </sanitizer>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
151 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
152 <param name="files" type="data" format="tabular" multiple="true" label="Counts file(s) at this time value" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
153 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
154 <repeat name="rep_groups" title="Experimental groups" min="1" default="1">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
155 <param name="name" type="text" value="Group title" label="Specify the name of this experimental group"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
156 help="Use a single name without spaces or special characters">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
157 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
158 <param name="files" type="data" format="tabular" multiple="true"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
159 label="Counts file(s) belonging to this experimental group" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
160 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
161 <repeat name="rep_repl" title="Replicates" min="0" default="0">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
162 <param name="files" type="data" format="tabular" multiple="true" label="Counts files that are replicates" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
163 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
164 </when>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
165 </conditional>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
166 <section name="makeDesignMatrix"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
167 title="Step 1: make.Design.Matrix - Defining the regression model"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
168 help="‘make.design.matrix’ creates the design matrix of dummies for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
169 fitting time series micorarray gene expression experiments.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
170 <param name="degree" type="integer" value="1"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
171 label="Degree of regression fit polynome"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
172 help="The degree of the regression fit polynome. ‘degree’ = 1 returns
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
173 linear regression, ‘degree’ = 2 returns quadratic regression, etc" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
174 </section>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
175 <section name="p_vector"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
176 title="Step 2: p.vector - Finding significant genes"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
177 help="‘p.vector’ performs a regression fit for each gene taking all
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
178 variables present in the model given by a regression matrix and
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
179 returns a list of FDR corrected significant genes">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
180 <param name="qvalue" type="float" value="0.05" label="Q" help="Significance level" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
181 <param name="min_obs" label="Minimum values" type="integer" value="6"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
182 help="Genes with less than this number of true numerical values
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
183 will be excluded from the analysis. Minimum value to estimate
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
184 the model is (degree+1)xGroups+1. Default is 6." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
185 </section>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
186 <section name="Tfit" title="Step 3: T.fit - Finding significant differences"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
187 help="‘T.fit’ selects the best regression model for each gene using
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
188 stepwise regression. In the maSigPro approach ‘p.vector’ and ‘T.fit’ are subsequent
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
189 steps, meaning that significant genes are first selected on the
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
190 basis of a general model and then the significant variables for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
191 each gene are found by step-wise regression.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
192 <param name="step_method" type="select" label="Step regression"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
193 help="The step regression can be ‘backward’ or ‘forward’ indicating
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
194 whether the step procedure starts from the model with all or none
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
195 variables. With the ‘two.ways.backward’ or ‘two.ways.forward’
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
196 options the variables are both allowed to get in and out. At each
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
197 step the p-value of each variable is computed and variables get
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
198 in/out the model when this p-value is lower or higher than given
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
199 threshold alfa.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
200 <option selected="True" value="backward">backward</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
201 <option value="forward">forward</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
202 <option value="two.ways.backward">two.ways.backward</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
203 <option value="two.ways.forward">two.ways.forward</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
204 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
205 <param type="boolean" name="nvar_correction" label="nvar correction" truevalue="TRUE" falsevalue="FALSE" checked="false"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
206 help="When nvar.correction is TRUE the given significance
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
207 level is corrected by the number of variables in the model.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
208 <option selected="True" value="FALSE">False</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
209 <option value="TRUE">True</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
210 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
211 <param name="alfa" type="float" value="0.05" label="alfa" help="Significance level used for variable selection in the stepwise regression" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
212 </section>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
213 <section name="getSiggenes"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
214 title="Step 4: get.siggenes - Obtaining lists of significant genes"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
215 help="This function creates lists of significant genes for a set of
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
216 variables whose significance value has been computed with the
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
217 ‘T.fit’ function.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
218 <param name="rsq" type="float" value="0.7" label="rsq"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
219 help="cut-off level at the R-squared value for the stepwise
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
220 regression fit. Only genes with R-squared more than rsq are
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
221 selected" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
222 <param name="vars" type="select" label="Variables"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
223 help="Variables for which to extract significant genes.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
224 ‘all’: generates one single matrix or gene list with all
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
225 significant genes.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
226
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
227 ‘each’: generates as many significant genes extractions as
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
228 variables in the general regression model. Each extraction
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
229 contains the significant genes for that variable.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
230
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
231 ‘groups’: generates a significant genes extraction for each
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
232 experimental group.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
233
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
234 The difference between ‘each’ and ‘groups’ is that in the
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
235 first case the variables of the same group (e.g. ‘TreatmentA’
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
236 and ‘time*TreatmentA’) will be extracted separately and in t
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
237 he
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
238 second case jointly.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
239 <option selected="True" value="groups">Groups</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
240 <option value="each">Each</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
241 <option value="all">All</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
242 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
243 <param name="significant_intercept" type="select" label="Significant intercept"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
244 help="The argument ‘significant.intercept’ modulates the treatment for
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
245 intercept coefficients to apply for selecting significant genes
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
246 when ‘vars’ equals ‘groups’. There are three possible values:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
247 ‘none’, no significant intercept (differences) are considered
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
248 for significant gene selection, ‘dummy’, includes genes with
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
249 significant intercept differences between control and experimental
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
250 groups, and ‘all’ when both significant intercept coefficient
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
251 for the control group and significant intercept differences are
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
252 considered for selecting significant genes.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
253 <option selected="True" value="dummy">Dummy</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
254 <option value="none">None</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
255 <option value="all">All</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
256 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
257 </section>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
258 <conditional name="pdf">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
259 <param label="Generate visualization PDF" name="pdf_selector" type="boolean"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
260 truevalue="1" falsevalue="0" checked="true"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
261 help="Choose if you want to generate a PDF file containing the visualizations" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
262 <when value="1">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
263 <section name="seeGenes" title="Step 5: see.genes - Visualization"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
264 help="This function provides visualisation tools for gene expression
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
265 values in a time course experiment. The function first calls the
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
266 heatmap function for a general overview of experiment results.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
267 Next a partioning of the data is generated using a clustering
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
268 method. The results of the clustering are visualized both as gene
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
269 expression profiles extended along all arrays in the experiment,
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
270 as provided by the plot.profiles function, and as summary
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
271 expression profiles for comparison among experimental groups.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
272 <param name="clusterData" label="Cluster Data" type="integer" value="1"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
273 help="Data clustering can be done on the basis of either the original
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
274 expression values, the regression coefficients, or the t.scores.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
275 In case ‘data’ is a ‘get.siggenes’ object, this is given by
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
276 providing the element names of the list
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
277 ‘c(sig.profiles,coefficients,t.score)’ of their list
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
278 position (1,2 or 3)." />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
279 <param name="k" type="integer" label="Number of clusters for data partioning" value="9" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
280 <conditional name="clustering">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
281 <param name="clusterMethod" label="Cluster Method" type="select"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
282 help="clustering method for data partioning. Currently
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
283 ‘hclust’, ‘kmeans’ and ‘Mclust’ are supported">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
284 <option selected="True" value="hclust">hclust</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
285 <option value="kmeans">kmeans</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
286 <option value="Mclust">Mclust</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
287 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
288 <when value="hclust">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
289 <param name="distance" type="select" label="Distance measure"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
290 help="Distance measurement function when ‘cluster.method’ is
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
291 ‘hclust’. Default uses correlation.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
292 <option selected="True" value="cor">Correlation</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
293 <option value="euclidean">Euclidean</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
294 <option value="maximum">Maximum</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
295 <option value="manhattan">Manhattan</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
296 <option value="Canberra">Canberra</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
297 <option value="binary">Binary</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
298 <option value="minkowski">Minkowski</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
299 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
300 <param name="aggloMethod" type="select" label="Agglomeration method"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
301 help="The agglomeration method to be used when ‘cluster.method’ is ‘hclust’.">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
302 <option selected="True" value="ward.D">ward.D</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
303 <option value="ward.D2">ward.D2</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
304 <option value="single">single</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
305 <option value="complete">complete</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
306 <option value="average">average (= UPGMA)</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
307 <option value="mcquitty">mcquitty (= WPGMA)</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
308 <option value="median">median (= WPGMC)</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
309 <option value="centroid">centroid (= UPGMC)</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
310 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
311 </when>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
312 <when value="kmeans">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
313 <param name="iterMax" type="integer" label="Maximum number of iterations" value="500"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
314 help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
315 </when>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
316 </conditional>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
317 <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
318 <option selected="True" value="rainbow">Rainbow</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
319 <option value="gray">Gray</option>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
320 </param>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
321 <param name="showFit" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show regression fit curves?"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
322 help="Indicating whether regression fit curves must be plotted" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
323 <param name="showLines" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw lines?"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
324 help="Indicating whether a line must be drawn joining plotted data points for each group" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
325 <param name="cexlab" type="float" value="0.8" label="Magnification for x labels"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
326 help="Graphical parameter maginfication to be used for x labels in plotting functions" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
327 <param name="legend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add legend to plotting profiles?"
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
328 help="Indicating whether legend must be added when plotting profiles" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
329 </section>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
330 </when>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
331 </conditional>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
332 </inputs>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
333 <outputs>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
334 <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
335 </data>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
336 <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
337 <filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
338 ((
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
339 source['source_selector'] == 'advanced' and
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
340 source['enable_output'] == True
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
341 ))
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
342 </filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
343 </data>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
344 <data format="txt" name="data_out" label="maSigPro data file on ${on_string}">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
345 <filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
346 ((
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
347 source['source_selector'] == 'advanced' and
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
348 source['enable_output'] == True
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
349 ))
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
350 </filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
351 </data>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
352 <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
353 <filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
354 ((
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
355 pdf['pdf_selector'] == True
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
356 ))
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
357 </filter>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
358 </data>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
359 </outputs>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
360 <tests>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
361 <test>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
362 <param name="source_selector" value="advanced" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
363 <param name="enable_output" value="1" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
364 <repeat name="rep_time">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
365 <param name="time" value="1" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
366 <param name="files" value="control_1H.counts,treat_1H.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
367 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
368 <repeat name="rep_time">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
369 <param name="time" value="2" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
370 <param name="files" value="control_2H.counts,treat_2H.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
371 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
372 <repeat name="rep_time">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
373 <param name="time" value="3" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
374 <param name="files" value="control_3H.counts,treat_3H_1.counts,treat_3H_2.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
375 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
376 <param name="replicates_selector" value="advanced" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
377 <repeat name="rep_repl">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
378 <param name="files" value="treat_3H_1.counts,treat_3H_2.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
379 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
380 <repeat name="rep_groups">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
381 <param name="name" value="Control" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
382 <param name="files" value="control_1H.counts,control_2H.counts,control_3H.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
383 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
384 <repeat name="rep_groups">
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
385 <param name="name" value="Treatment" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
386 <param name="files" value="treat_1H.counts,treat_2H.counts,treat_3H_1.counts,treat_3H_2.counts" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
387 </repeat>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
388 <output name="masigpro_out" file="masigpro_out.tab" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
389 <output name="data_out" file="data_out.txt" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
390 <output name="edesign_out" file="edesign_out.txt" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
391 <output name="pdf_out" file="Results.pdf" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
392 </test>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
393 <test>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
394 <param name="source_selector" value="defaults" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
395 <param name="edesign" value="edesign_out.txt" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
396 <param name="data" value="data_out.txt" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
397 <output name="masigpro_out" file="masigpro_out.tab" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
398 <output name="pdf_out" file="Results.pdf" />
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
399 </test>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
400 </tests>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
401 <help>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
402 <![CDATA[
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
403 .. class:: infomark
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
404
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
405 **What it does**
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
406
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
407 maSigPro_ is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
408
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
409 **Inputs**
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
410
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
411 The maSigPro wrapper has two options for input data:
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
412
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
413 - directly through two seperate text files containing the experiment design (edesign) and the data or
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
414 - count tables generated from HTSeq-count. Count tables must be generated for each sample individually.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
415
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
416 To set up an experimental design from seperate count files you first have to select which files belong to a certain time point.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
417 Likewise you can specify which files are replicates. In a third step you have to create the experimental groups and select the related files.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
418 For a more comfortable setup in future analysis you have the option to output the generated edesign and data files.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
419
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
420 **Output**
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
421
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
422 maSigPro_ generates a summary file containing the list of significant genes. Additionally you can obtain a PDF file containing plots of profiles and groups that visualize the clustering analysis.
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
423
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
424 .. _maSigPro: https://bioconductor.org/packages/release/bioc/html/maSigPro.html
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
425 ]]>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
426 </help>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
427 <citations>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
428 <citation type="doi">10.1093/bioinformatics/btl056</citation>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
429 </citations>
c8c290f3ea7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
iuc
parents:
diff changeset
430 </tool>