masigpro: masigpro.xml annotate

annotate masigpro.xml @ 4:21a81335cd13 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

author	iuc
date	Tue, 31 Aug 2021 09:21:26 +0000
parents	a9c93cd4f54b
children	401e7c9e09f2

rev	line source
3 a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	1 <tool id="masigpro" name="maSigPro" version="1.49.3.1+galaxy1">
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	2 <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>
4 21a81335cd13 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 3 diff changeset	3 <xrefs>
21a81335cd13 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 3 diff changeset	4 <xref type="bio.tools">masigpro</xref>
21a81335cd13 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 3 diff changeset	5 </xrefs>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	6 <requirements>
3 a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	7 <requirement type="package" version="8.25">coreutils</requirement>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	8 <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	9 <requirement type="package" version="1.3.2">r-optparse</requirement>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	10 <requirement type="package" version="4.4">sed</requirement>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	11 </requirements>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	12 <stdio>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	13 <regex match="Execution halted"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	14 source="both"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	15 level="fatal"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	16 description="Execution halted." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	17 <regex match="Error in"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	18 source="both"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	19 level="fatal"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	20 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	21 <regex match="Fatal error"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	22 source="both"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	23 level="fatal"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	24 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	25 </stdio>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	26 <version_command>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	27 <![CDATA[
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	28 echo $(R --version \| grep version \| grep -v GNU)", maSigPro version" $(R --vanilla --slave -e "library(maSigPro); cat(sessionInfo()\$otherPkgs\$maSigPro\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	29 ]]>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	30 </version_command>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	31 <command>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	32 <![CDATA[
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	33 #if str($source.source_selector) == "advanced":
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	34 paste
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	35 #set $start = True
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	36 #set $header = ''
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	37 #for $time in $source.rep_time:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	38 #for $file in $time.files:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	39 #if $start:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	40 <(cut -f1 $file)
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	41 #set $start = False
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	42 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	43 #set $header += ' "' + $file.name + '"'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	44 <(cut -f2 $file)
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	45 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	46 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	47 > data && sed -i '1i$header' data &&
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	48 #if $source.enable_output:
3 a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	49 cp $design_matrix $edesign_out &&
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	50 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	51 #set $data = 'data'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	52 #set $edesign = $design_matrix
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	53 #else:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	54 #set $data = $source.data
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	55 #set $edesign = $source.edesign
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	56 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	57 Rscript '${__tool_directory__}/masigpro.R'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	58 -e '$edesign'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	59 -d '$data'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	60 -o '$masigpro_out'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	61 #if str($source.source_selector) == "defaults":
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	62 --time_col $source.time_col
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	63 --repl_col $source.repl_col
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	64 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	65 --degree $makeDesignMatrix.degree
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	66 --qvalue $p_vector.qvalue
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	67 --min_obs $p_vector.min_obs
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	68 --step_method '$Tfit.step_method'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	69 --nvar_correction $Tfit.nvar_correction
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	70 --alfa $Tfit.alfa
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	71 --rsq $getSiggenes.rsq
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	72 --vars '$getSiggenes.vars'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	73 --significant_intercept '$getSiggenes.significant_intercept'
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	74 #if $pdf.pdf_selector:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	75 --cluster_data $pdf.seeGenes.clusterData
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	76 -k $pdf.seeGenes.k
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	77 --print_cluster $pdf.seeGenes.print_cluster
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	78 --cluster_method $pdf.seeGenes.clustering.clusterMethod
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	79 #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust":
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	80 --distance $pdf.seeGenes.clustering.distance
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	81 --agglo_method $pdf.seeGenes.clustering.aggloMethod
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	82 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	83 #if str($pdf.seeGenes.clustering.clusterMethod) == "kmeans":
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	84 --iter_max $pdf.seeGenes.clustering.iterMax
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	85 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	86 --color_mode $pdf.seeGenes.colorMode
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	87 --show_fit $pdf.seeGenes.showFit
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	88 --show_lines $pdf.seeGenes.showLines
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	89 --cexlab $pdf.seeGenes.cexlab
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	90 --legend $pdf.seeGenes.legend
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	91 #end if
3 a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	92 #if str($source.source_selector) == "advanced" and $source.enable_output
a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	93 && mv data $data_out
a9c93cd4f54b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f" iuc parents: 2 diff changeset	94 #end if
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	95 ]]>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	96 </command>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	97 <configfiles>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	98 <configfile name="design_matrix">#if str($source.source_selector) == "advanced":
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	99 #set $header = "Name Time Replicate"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	100 #for $group in $source.rep_groups:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	101 #set $header = $header + ' ' + str($group.name)
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	102 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	103 $header
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	104 #set $c = len($source.rep_repl) + 1
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	105 #for $time in $source.rep_time:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	106 #for $file in $time.files:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	107 #set $is_repl = False
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	108 #for $i, $repl in enumerate($source.rep_repl):
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	109 #if str($file) in str($repl.files):
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	110 #set $r = $i + 1
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	111 #set $is_repl = True
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	112 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	113 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	114 #if $is_repl == False:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	115 #set $r = $c
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	116 #set $c += 1
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	117 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	118 #set $line = '"' + str($file.name) + '" ' + str($time.time) + ' ' + str($r)
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	119 #for $group in $source.rep_groups:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	120 #if str($file) in str($group.files):
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	121 #set $line += " 1"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	122 #else
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	123 #set $line += " 0"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	124 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	125 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	126 $line
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	127 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	128 #end for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	129 #end if
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	130 </configfile>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	131 </configfiles>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	132 <inputs>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	133 <conditional name="source">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	134 <param label="Choose data source" name="source_selector"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	135 help="Choose if you want to provide seperate count files (e.g. from HTSeq-count or feature-seq)
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	136 and define your experiment design matrix here, or if you have maSigPro edesign and data input files already."
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	137 type="select">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	138 <option value="defaults">Use maSigPro edesign and data files</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	139 <option value="advanced">Seperate count data (e.g. from HTSeq-count or feature-count)</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	140 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	141 <when value="defaults">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	142 <param name="edesign" format="tabular,txt" type="data" label="Experiment matrix"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	143 help="Matrix describing experimental design. Rows must be arrays and columns experiment descriptors" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	144 <param name="data" format="tabular,txt" type="data" label="Gene expression matrix"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	145 help="Matrix containing normalized gene expression data. Genes must be in rows and arrays in columns" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	146 <param name="time_col" label="Column number containing time values" type="integer" value="1"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	147 help="Column number in edesign containing time values. Default is first column" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	148 <param name="repl_col" label="Column number containing replicate coding" type="integer" value="2"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	149 help="Column number in edesign containing coding for replicate arrays. Default is second column" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	150 </when>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	151 <when value="advanced">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	152 <param name="enable_output" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output generated maSigPro input files?"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	153 help="Choose if you want to output the generated edesign and data files for direct use in maSigPro as history elements." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	154 <repeat name="rep_time" title="Time values" min="1" default="1">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	155 <param name="time" type="integer" value="0" label="Specify a numerical time value" help="Only numbers will be allowed">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	156 <sanitizer>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	157 <valid initial="string.digits"></valid>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	158 </sanitizer>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	159 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	160 <param name="files" type="data" format="tabular" multiple="true" label="Counts file(s) at this time value" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	161 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	162 <repeat name="rep_groups" title="Experimental groups" min="1" default="1">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	163 <param name="name" type="text" value="Group title" label="Specify the name of this experimental group"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	164 help="Use a single name without spaces or special characters">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	165 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	166 <param name="files" type="data" format="tabular" multiple="true"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	167 label="Counts file(s) belonging to this experimental group" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	168 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	169 <repeat name="rep_repl" title="Replicates" min="0" default="0">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	170 <param name="files" type="data" format="tabular" multiple="true" label="Counts files that are replicates" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	171 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	172 </when>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	173 </conditional>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	174 <section name="makeDesignMatrix"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	175 title="Step 1: make.Design.Matrix - Defining the regression model"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	176 help="‘make.design.matrix’ creates the design matrix of dummies for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	177 fitting time series micorarray gene expression experiments.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	178 <param name="degree" type="integer" value="1"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	179 label="Degree of regression fit polynome"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	180 help="The degree of the regression fit polynome. ‘degree’ = 1 returns
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	181 linear regression, ‘degree’ = 2 returns quadratic regression, etc" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	182 </section>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	183 <section name="p_vector"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	184 title="Step 2: p.vector - Finding significant genes"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	185 help="‘p.vector’ performs a regression fit for each gene taking all
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	186 variables present in the model given by a regression matrix and
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	187 returns a list of FDR corrected significant genes">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	188 <param name="qvalue" type="float" value="0.05" label="Q" help="Significance level" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	189 <param name="min_obs" label="Minimum values" type="integer" value="6"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	190 help="Genes with less than this number of true numerical values
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	191 will be excluded from the analysis. Minimum value to estimate
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	192 the model is (degree+1)xGroups+1. Default is 6." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	193 </section>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	194 <section name="Tfit" title="Step 3: T.fit - Finding significant differences"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	195 help="‘T.fit’ selects the best regression model for each gene using
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	196 stepwise regression. In the maSigPro approach ‘p.vector’ and ‘T.fit’ are subsequent
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	197 steps, meaning that significant genes are first selected on the
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	198 basis of a general model and then the significant variables for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	199 each gene are found by step-wise regression.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	200 <param name="step_method" type="select" label="Step regression"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	201 help="The step regression can be ‘backward’ or ‘forward’ indicating
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	202 whether the step procedure starts from the model with all or none
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	203 variables. With the ‘two.ways.backward’ or ‘two.ways.forward’
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	204 options the variables are both allowed to get in and out. At each
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	205 step the p-value of each variable is computed and variables get
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	206 in/out the model when this p-value is lower or higher than given
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	207 threshold alfa.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	208 <option selected="True" value="backward">backward</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	209 <option value="forward">forward</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	210 <option value="two.ways.backward">two.ways.backward</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	211 <option value="two.ways.forward">two.ways.forward</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	212 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	213 <param type="boolean" name="nvar_correction" label="nvar correction" truevalue="TRUE" falsevalue="FALSE" checked="false"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	214 help="When nvar.correction is TRUE the given significance
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	215 level is corrected by the number of variables in the model.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	216 <option selected="True" value="FALSE">False</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	217 <option value="TRUE">True</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	218 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	219 <param name="alfa" type="float" value="0.05" label="alfa" help="Significance level used for variable selection in the stepwise regression" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	220 </section>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	221 <section name="getSiggenes"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	222 title="Step 4: get.siggenes - Obtaining lists of significant genes"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	223 help="This function creates lists of significant genes for a set of
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	224 variables whose significance value has been computed with the
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	225 ‘T.fit’ function.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	226 <param name="rsq" type="float" value="0.7" label="rsq"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	227 help="cut-off level at the R-squared value for the stepwise
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	228 regression fit. Only genes with R-squared more than rsq are
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	229 selected" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	230 <param name="vars" type="select" label="Variables"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	231 help="Variables for which to extract significant genes.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	232 ‘all’: generates one single matrix or gene list with all
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	233 significant genes.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	234
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	235 ‘each’: generates as many significant genes extractions as
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	236 variables in the general regression model. Each extraction
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	237 contains the significant genes for that variable.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	238
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	239 ‘groups’: generates a significant genes extraction for each
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	240 experimental group.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	241
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	242 The difference between ‘each’ and ‘groups’ is that in the
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	243 first case the variables of the same group (e.g. ‘TreatmentA’
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	244 and ‘time*TreatmentA’) will be extracted separately and in t
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	245 he
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	246 second case jointly.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	247 <option selected="True" value="groups">Groups</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	248 <option value="each">Each</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	249 <option value="all">All</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	250 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	251 <param name="significant_intercept" type="select" label="Significant intercept"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	252 help="The argument ‘significant.intercept’ modulates the treatment for
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	253 intercept coefficients to apply for selecting significant genes
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	254 when ‘vars’ equals ‘groups’. There are three possible values:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	255 ‘none’, no significant intercept (differences) are considered
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	256 for significant gene selection, ‘dummy’, includes genes with
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	257 significant intercept differences between control and experimental
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	258 groups, and ‘all’ when both significant intercept coefficient
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	259 for the control group and significant intercept differences are
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	260 considered for selecting significant genes.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	261 <option selected="True" value="dummy">Dummy</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	262 <option value="none">None</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	263 <option value="all">All</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	264 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	265 </section>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	266 <conditional name="pdf">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	267 <param label="Generate visualization PDF" name="pdf_selector" type="boolean"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	268 truevalue="1" falsevalue="0" checked="true"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	269 help="Choose if you want to generate a PDF file containing the visualizations" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	270 <when value="1">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	271 <section name="seeGenes" title="Step 5: see.genes - Visualization"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	272 help="This function provides visualisation tools for gene expression
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	273 values in a time course experiment. The function first calls the
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	274 heatmap function for a general overview of experiment results.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	275 Next a partioning of the data is generated using a clustering
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	276 method. The results of the clustering are visualized both as gene
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	277 expression profiles extended along all arrays in the experiment,
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	278 as provided by the plot.profiles function, and as summary
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	279 expression profiles for comparison among experimental groups.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	280 <param name="clusterData" label="Cluster Data" type="integer" value="1"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	281 help="Data clustering can be done on the basis of either the original
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	282 expression values, the regression coefficients, or the t.scores.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	283 In case ‘data’ is a ‘get.siggenes’ object, this is given by
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	284 providing the element names of the list
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	285 ‘c(sig.profiles,coefficients,t.score)’ of their list
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	286 position (1,2 or 3)." />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	287 <param name="k" type="integer" label="Number of clusters for data partioning" value="9" />
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	288 <param name="print_cluster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	289 label="Add cluster information to summary file?"
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	290 help="Adds columns with the cluster assignment for each gene." />
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	291 <conditional name="clustering">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	292 <param name="clusterMethod" label="Cluster Method" type="select"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	293 help="clustering method for data partioning. Currently
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	294 ‘hclust’, ‘kmeans’ and ‘Mclust’ are supported">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	295 <option selected="True" value="hclust">hclust</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	296 <option value="kmeans">kmeans</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	297 <option value="Mclust">Mclust</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	298 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	299 <when value="hclust">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	300 <param name="distance" type="select" label="Distance measure"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	301 help="Distance measurement function when ‘cluster.method’ is
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	302 ‘hclust’. Default uses correlation.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	303 <option selected="True" value="cor">Correlation</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	304 <option value="euclidean">Euclidean</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	305 <option value="maximum">Maximum</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	306 <option value="manhattan">Manhattan</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	307 <option value="Canberra">Canberra</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	308 <option value="binary">Binary</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	309 <option value="minkowski">Minkowski</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	310 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	311 <param name="aggloMethod" type="select" label="Agglomeration method"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	312 help="The agglomeration method to be used when ‘cluster.method’ is ‘hclust’.">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	313 <option selected="True" value="ward.D">ward.D</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	314 <option value="ward.D2">ward.D2</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	315 <option value="single">single</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	316 <option value="complete">complete</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	317 <option value="average">average (= UPGMA)</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	318 <option value="mcquitty">mcquitty (= WPGMA)</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	319 <option value="median">median (= WPGMC)</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	320 <option value="centroid">centroid (= UPGMC)</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	321 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	322 </when>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	323 <when value="kmeans">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	324 <param name="iterMax" type="integer" label="Maximum number of iterations" value="500"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	325 help="Maximum number of iterations when ‘cluster.method’ is ‘kmeans’" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	326 </when>
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	327 <when value="Mclust">
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	328 </when>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	329 </conditional>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	330 <param name="colorMode" label="Color Mode" type="select" help="Color scale for plotting profiles. Can be either ‘rainbow’ or ‘gray’">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	331 <option selected="True" value="rainbow">Rainbow</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	332 <option value="gray">Gray</option>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	333 </param>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	334 <param name="showFit" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Show regression fit curves?"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	335 help="Indicating whether regression fit curves must be plotted" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	336 <param name="showLines" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Draw lines?"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	337 help="Indicating whether a line must be drawn joining plotted data points for each group" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	338 <param name="cexlab" type="float" value="0.8" label="Magnification for x labels"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	339 help="Graphical parameter maginfication to be used for x labels in plotting functions" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	340 <param name="legend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Add legend to plotting profiles?"
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	341 help="Indicating whether legend must be added when plotting profiles" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	342 </section>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	343 </when>
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	344 <when value="0">
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	345 </when>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	346 </conditional>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	347 </inputs>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	348 <outputs>
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	349 <data format="txt" name="data_out" label="maSigPro data file on ${on_string}">
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	350 <filter>
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	351 ((
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	352 source['source_selector'] == 'advanced' and
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	353 source['enable_output'] == True
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	354 ))
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	355 </filter>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	356 </data>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	357 <data format="txt" name="edesign_out" label="maSigPro edesign file on ${on_string}">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	358 <filter>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	359 ((
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	360 source['source_selector'] == 'advanced' and
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	361 source['enable_output'] == True
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	362 ))
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	363 </filter>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	364 </data>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	365 <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	366 <filter>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	367 ((
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	368 pdf['pdf_selector'] == True
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	369 ))
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	370 </filter>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	371 </data>
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	372 <data format="tabular" name="masigpro_out" label="maSigPro result file on ${on_string}">
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	373 </data>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	374 </outputs>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	375 <tests>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	376 <test>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	377 <param name="source_selector" value="advanced" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	378 <param name="enable_output" value="1" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	379 <repeat name="rep_time">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	380 <param name="time" value="1" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	381 <param name="files" value="control_1H.counts,treat_1H.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	382 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	383 <repeat name="rep_time">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	384 <param name="time" value="2" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	385 <param name="files" value="control_2H.counts,treat_2H.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	386 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	387 <repeat name="rep_time">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	388 <param name="time" value="3" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	389 <param name="files" value="control_3H.counts,treat_3H_1.counts,treat_3H_2.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	390 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	391 <param name="replicates_selector" value="advanced" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	392 <repeat name="rep_repl">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	393 <param name="files" value="treat_3H_1.counts,treat_3H_2.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	394 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	395 <repeat name="rep_groups">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	396 <param name="name" value="Control" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	397 <param name="files" value="control_1H.counts,control_2H.counts,control_3H.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	398 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	399 <repeat name="rep_groups">
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	400 <param name="name" value="Treatment" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	401 <param name="files" value="treat_1H.counts,treat_2H.counts,treat_3H_1.counts,treat_3H_2.counts" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	402 </repeat>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	403 <output name="masigpro_out" file="masigpro_out.tab" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	404 <output name="data_out" file="data_out.txt" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	405 <output name="edesign_out" file="edesign_out.txt" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	406 <output name="pdf_out" file="Results.pdf" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	407 </test>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	408 <test>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	409 <param name="source_selector" value="defaults" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	410 <param name="edesign" value="edesign_out.txt" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	411 <param name="data" value="data_out.txt" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	412 <output name="masigpro_out" file="masigpro_out.tab" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	413 <output name="pdf_out" file="Results.pdf" />
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	414 </test>
2 0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	415 <test>
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	416 <param name="source_selector" value="defaults" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	417 <param name="edesign" value="edesign_out.txt" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	418 <param name="data" value="data_out.txt" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	419 <param name="print_cluster" value="FALSE" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	420 <output name="masigpro_out" file="masigpro_out_no_cluster.tab" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	421 <output name="pdf_out" file="Results.pdf" />
0e5ddeb06378 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231 iuc parents: 1 diff changeset	422 </test>
1 6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	423 </tests>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	424 <help>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	425 <![CDATA[
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	426 .. class:: infomark
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	427
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	428 What it does
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	429
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	430 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.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	431
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	432 Inputs
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	433
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	434 The maSigPro wrapper has two options for input data:
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	435
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	436 - directly through two seperate text files containing the experiment design (edesign) and the data or
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	437 - count tables generated from HTSeq-count. Count tables must be generated for each sample individually.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	438
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	439 To set up an experimental design from seperate count files you first have to select which files belong to a certain time point.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	440 Likewise you can specify which files are replicates. In a third step you have to create the experimental groups and select the related files.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	441 For a more comfortable setup in future analysis you have the option to output the generated edesign and data files.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	442
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	443 Output
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	444
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	445 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.
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	446
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	447 .. _maSigPro: https://bioconductor.org/packages/release/bioc/html/maSigPro.html
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	448 ]]>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	449 </help>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	450 <citations>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	451 <citation type="doi">10.1093/bioinformatics/btl056</citation>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	452 </citations>
6bc58c43b997 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit c4510bf402d10e8e3a3c4c90c2d96666c987a256 iuc parents: 0 diff changeset	453 </tool>

Mercurial > repos > iuc > masigpro

annotate masigpro.xml @ 4:21a81335cd13 draft