cummerbund: cummeRbund.xml annotate

annotate cummeRbund.xml @ 2:4bbfacecedd3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"

author	devteam
date	Mon, 06 Jul 2020 18:11:20 +0000
parents	aefbcaf15a94
children

rev	line source
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	1 <?xml version="1.0"?>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	2 <tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	3 <description>visualize Cuffdiff output</description>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	4 <macros>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	5 <import>cummeRbund_macros.xml</import>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	6 </macros>
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	7 <requirements>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	8 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	9 <requirement type="package" version="1.0.4">r-argparse</requirement>
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	10 <requirement type="package" version="3.4.1">r-base</requirement>
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	12 </requirements>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	13 <code file="cummeRbund_options.py"/>
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	14 <command detect_errors="aggressive">
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	15 <![CDATA[
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	16 #for i, p in enumerate($plots):
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	17 Rscript --vanilla --slave '$__tool_directory__/cummeRbund.R'
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	18 --input '$input_database' --width $p.width --height $p.height --type "${p.plot.type}"
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	19 --outfile 'plot-${p.plot.type}-${i}.png'
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	21 $p.plot.replicates
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	22 #elif $p.plot.type == "scatter":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	25 --features $p.plot.multiple_genes.features --gene_selector
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	26 #for gene in $p.plot.multiple_genes.genes:
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	27 --genes '$gene.gene_id'
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	28 #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	29 #end if
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	30 #elif $p.plot.type == "maplot":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	32 #elif $p.plot.type == "volcano":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	33 --x "$p.plot.x" --y "$p.plot.y"
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	35 --features $p.plot.multiple_genes.features --gene_selector
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	36 #for gene in $p.plot.multiple_genes.genes:
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	37 --genes '$gene.gene_id'
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	38 #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	39 #end if
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	40 #elif $p.plot.type == "heatmap":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	42 #if len($p.plot.genes) > 0:
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	43 --gene_selector
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	44 #for gene in $p.plot.genes:
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	45 --genes '$gene.gene_id'
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	46 #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	47 #end if
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	48 #elif $p.plot.type == "cluster":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	49 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	50 #if len($p.plot.genes) > 0:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	51 #for gene in $p.plot.genes:
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	52 --genes '$gene.gene_id'
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	53 #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	54 #end if
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	55 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	56 #if $p.plot.type == "expressionplot":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	57 $p.plot.draw_summary
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	58 #end if
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	59 --features $p.plot.features $p.plot.error_bars --genes '$p.plot.gene_id' $p.plot.replicates $p.plot.log10
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	60 #end if
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	61 #if $p.plot.type == "density":
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	62 $p.plot.log10
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	63 #end if
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	64 > '${output}' 2>&1 ;
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	65 #end for
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	66 ]]></command>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	67 <inputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	68 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	69 <repeat name="plots" title="Plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 <param name="width" type="integer" value="1280" label="The width of the image"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	71 <param name="height" type="integer" value="960" label="The height of the image"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	72 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	73 <param name="type" type="select" label="Plot type">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	74 <option value="density" selected="true">Density</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	75 <option value="boxplot">Boxplot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	76 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	77 <option value="pca">Principal Component Analysis (PCA) Plot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	78 <option value="dendrogram">Dendrogram</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	79 <option value="scatter">Scatter</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	80 <option value="volcano">Volcano</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 <option value="heatmap">Heatmap</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	82 <option value="dispersion">Dispersion</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	83 <option value="fpkmSCV">Squared Coefficient of Variation</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	84 <option value="scatterMatrix">Scatter Matrix</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	85 <option value="cluster">Cluster</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	86 <option value="expressionplot">Expression Plot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	87 <option value="expressionbarplot">Expression Bar Plot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	88 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	89 </param>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	90 <when value="density">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	91 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	92 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	93 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	94 <when value="mds">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	96 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	97 <when value="pca">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	100 <when value="boxplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	101 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	102 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	103 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	104 <when value="dendrogram">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	105 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	106 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	107 <when value="scatter">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	108 <expand macro="xy_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	109 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	110 <param name="smooth" type="boolean" truevalue="--smooth" falsevalue="" checked="True" label="Add a smooth-fit regression line"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	111 <expand macro="multiple_genes_conditional" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	112 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	113 <when value="volcano">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	114 <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	115 <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	116 <expand macro="multiple_genes_conditional" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	117 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 <when value="heatmap">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 <expand macro="genes_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	121 <param name="clustering" type="select" label="Cluster by">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	122 <option value="row">Row</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	123 <option value="column">Column</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	124 <option value="both" selected="true">Both</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	125 <option value="none">None</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	126 </param>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	127 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	128 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display row labels?"/>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	129 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	130 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	131 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	132 <when value="cluster">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	133 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 <expand macro="genes_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	135 <param name="k" type="integer" value="1" label="Number of pre-defined clusters to attempt to find."/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	136 <param name="iter_max" type="integer" value="100" label="Max iterations"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	137 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	138 <when value="maplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	139 <expand macro="xy_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	140 <param name="count" type="boolean" truevalue="--count" falsevalue="" checked="False" label="Use Count?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	141 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	142 <when value="dispersion" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	143 <when value="fpkmSCV" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	144 <when value="scatterMatrix" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 <when value="expressionplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	147 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	148 <param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	149 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	150 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	151 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	152 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	153 <when value="expressionbarplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	154 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	155 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	156 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	157 <expand macro="replicates_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	158 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	159 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	161 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	162 </inputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	163 <outputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	164 <data format="txt" name="output" label="${tool.name} on ${on_string}">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	165 <discover_datasets pattern="plot-(?P<designation>.+)\.png" ext="png" visible="true" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166 </data>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	167 </outputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	168 <tests>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	169 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	170 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	171 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	172 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	175 <param name="type" value="maplot" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	176 <param name="x" value="q1" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	177 <param name="y" value="q2" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	178 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	179 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	180 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	181 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	182 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	183 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	184 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	186 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	187 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	188 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	191 <param name="type" value="scatter" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	192 <param name="x" value="q1" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	193 <param name="y" value="q2" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	194 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	195 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	196 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	197 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	199 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	200 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	202 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	203 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	205 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	206 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207 <param name="type" value="dispersion" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	208 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	209 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	210 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	211 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	216 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	217 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	218 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	219 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	220 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 <param name="type" value="scatterMatrix" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	222 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	223 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	224 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	225 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	226 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	227 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	229 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	230 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	231 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	234 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	235 <param name="type" value="pca" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	236 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	237 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	238 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	239 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	240 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249 <param name="type" value="expressionplot" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 <param name="features" value="gene" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 <param name="gene_id" value="XLOC_000059" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	254 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	255 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	259 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	260 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	265 <param name="features" value="gene" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	266 <param name="type" value="expressionbarplot" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	267 <param name="gene_id" value="XLOC_000039" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	268 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	269 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	270 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	271 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	272 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	273 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	274 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	275 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	276 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	277 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	278 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	279 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	280 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	281 <param name="type" value="heatmap" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	282 <repeat name="genes">
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	283 <param name="gene_id" value="XLOC_000030" />
aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	284 </repeat>
aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	285 <repeat name="genes">
aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	286 <param name="gene_id" value="XLOC_000037" />
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	288 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	289 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	290 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	291 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	292 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	293 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	294 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	295 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	296 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	297 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	298 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	299 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	301 <param name="type" value="density" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	302 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	303 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	304 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	305 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	306 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	307 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	308 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	309 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	310 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	311 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	315 <param name="type" value="dendrogram" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	316 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	317 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	318 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	319 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	320 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	321 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	322 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	323 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	324 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	325 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	328 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	329 <param name="type" value="volcano" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	330 <param name="x" value="q1" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	331 <param name="y" value="q2" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	332 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	333 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	334 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	335 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	336 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	337 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	338 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	339 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	340 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	341 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	342 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	343 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	344 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	345 <param name="type" value="boxplot" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	346 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	347 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	348 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	349 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	350 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	351 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	352 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	353 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	354 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	355 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	356 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	357 <param name="height" value="960" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	358 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	359 <param name="type" value="fpkmSCV" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	360 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	361 </repeat>
2 4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	362 <output name="output" ftype="txt">
4bbfacecedd3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24" devteam parents: 1 diff changeset	363 <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	364 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	365 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	366 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	367 </tests>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	368 <help><![CDATA[
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	369 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	370
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	371 ------
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	372
1 aefbcaf15a94 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3 devteam parents: 0 diff changeset	373 Based on the `cummeRbund wrapper <https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
0 e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	374 ]]></help>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	375 <citations>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	376 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	377 </citations>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	378 </tool>

Mercurial > repos > devteam > cummerbund

annotate cummeRbund.xml @ 2:4bbfacecedd3 draft default tip