cummerbund: cummeRbund.xml annotate

annotate cummeRbund.xml @ 2:ac2ebc60ef5d draft

Uploaded corrected dynamic options

author	devteam
date	Mon, 16 Mar 2015 15:43:02 -0400
parents	587c425b4e76
children	3a0ade59306a

rev	line source
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	1 <?xml version="1.0"?>
2 ac2ebc60ef5d Uploaded corrected dynamic options devteam parents: 0 diff changeset	2 <tool id="cummeRbund" name="Plot CuffDiff" version="1.0.1">
0 587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	3 <description>data with cummeRbund</description>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	4 <requirements>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	5 <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	6 <requirement type="package" version="3.1.2">R</requirement>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	7 <requirement type="package" version="2.8.2">cummeRbund</requirement>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	8 </requirements>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	9 <expand macro="stdio" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	10 <macros>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	11 <import>cummeRbund_macros.xml</import>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	12 </macros>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	13 <code file="cummeRbund_options.py"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	14 <command>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	15 <![CDATA[
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	16 #for i, p in enumerate($plots):
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	17 R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	18 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	19 --outfile plot-${p.plot.type}-${i}.png
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	21 $p.plot.replicates
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	22 #elif $p.plot.type == "scatter":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	25 --features $p.plot.multiple_genes.features --gene_selector
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	26 #for gene in $p.plot.multiple_genes.genes:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	27 --genes ${gene.gene_id}
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	28 #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	29 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	30 #elif $p.plot.type == "maplot":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	32 #elif $p.plot.type == "volcano":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	33 --x "$p.plot.x" --y "$p.plot.y"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	35 --features $p.plot.multiple_genes.features --gene_selector
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	36 #for gene in $p.plot.multiple_genes.genes:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	37 --genes ${gene.gene_id}
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	38 #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	39 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	40 #elif $p.plot.type == "heatmap":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	42 #if len($p.plot.genes) > 0:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	43 #for gene in $p.plot.genes:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	44 --genes ${gene.gene_id}
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	45 #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	46 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	47 #elif $p.plot.type == "cluster":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	48 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	49 #if len($p.plot.genes) > 0:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	50 #for gene in $p.plot.genes:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	51 --genes ${gene.gene_id}
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	52 #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	53 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	54 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	55 #if $p.plot.type == "expressionplot":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	56 $p.plot.draw_summary
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	57 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	58 --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	59 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	60 #if $p.plot.type == "density":
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	61 $p.plot.log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	62 #end if
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	63 > "${output}" 2>&1 ;
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	64 #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	65 ]]></command>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	66 <inputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	67 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	68 <repeat name="plots" title="Plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	69 <param name="width" type="integer" value="1280" label="The width of the image"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	70 <param name="height" type="integer" value="960" label="The height of the image"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	71 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	72 <param name="type" type="select" label="Plot type">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	73 <option value="density" selected="true">Density</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	74 <option value="boxplot">Boxplot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	75 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	76 <option value="pca">Principal Component Analysis (PCA) Plot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	77 <option value="dendrogram">Dendrogram</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	78 <option value="scatter">Scatter</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	79 <option value="volcano">Volcano</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	80 <option value="heatmap">Heatmap</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	81 <option value="dispersion">Dispersion</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	82 <option value="fpkmSCV">Squared Coefficient of Variation</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	83 <option value="scatterMatrix">Scatter Matrix</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	84 <option value="cluster">Cluster</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	85 <option value="expressionplot">Expression Plot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	86 <option value="expressionbarplot">Expression Bar Plot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	87 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	88 </param>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	89 <when value="density">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	90 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	91 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	92 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	93 <when value="mds">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	94 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	95 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	96 <when value="pca">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	97 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	98 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	99 <when value="boxplot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	100 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	101 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	102 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	103 <when value="dendrogram">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	104 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	105 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	106 <when value="scatter">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	107 <expand macro="xy_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	108 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	109 <param name="smooth" type="boolean" truevalue="--smooth" falsevalue="" checked="True" label="Add a smooth-fit regression line"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	110 <expand macro="multiple_genes_conditional" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	111 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	112 <when value="volcano">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	113 <param name="x" type="select" label="First sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	114 <param name="y" type="select" label="Second sample name for comparison" dynamic_options="get_samples(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	115 <expand macro="multiple_genes_conditional" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	116 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	117 <when value="heatmap">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	118 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	119 <expand macro="genes_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	120 <param name="clustering" type="select" label="Cluster by">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	121 <option value="row">Row</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	122 <option value="column">Column</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	123 <option value="both" selected="true">Both</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	124 <option value="none">None</option>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	125 </param>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	126 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	127 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	128 <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	129 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	130 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	131 <when value="cluster">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	132 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	133 <expand macro="genes_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	134 <param name="k" type="integer" value="1" label="Number of pre-defined clusters to attempt to find."/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	135 <param name="iter_max" type="integer" value="100" label="Max iterations"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	136 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	137 <when value="maplot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	138 <expand macro="xy_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	139 <param name="count" type="boolean" truevalue="--count" falsevalue="" checked="False" label="Use Count?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	140 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	141 <when value="dispersion" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	142 <when value="fpkmSCV" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	143 <when value="scatterMatrix" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	144 <when value="expressionplot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	145 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	146 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	147 <param name="draw_summary" type="boolean" truevalue="--summary" falsevalue="" checked="False" label="Draw a 'summary' line with mean FPKM values for each condition?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	148 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	149 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	150 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	151 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	152 <when value="expressionbarplot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	153 <expand macro="features_selector" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	154 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	155 <param name="error_bars" type="boolean" truevalue="--error_bars" falsevalue="" checked="True" label="Draw error bars?"/>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	156 <expand macro="replicates_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	157 <expand macro="log10_checkbox" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	158 </when>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	159 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	160 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	161 </inputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	162 <outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	163 <data format="txt" name="output" label="${tool.name} on ${on_string}">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	164 <discover_datasets pattern="plot-(?P<designation>.+)\.png" ext="png" visible="true" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	165 </data>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	166 </outputs>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	167 <tests>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	168 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	169 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	170 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	171 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	172 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	173 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	174 <param name="type" value="maplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	175 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	176 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	177 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	178 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	179 <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	180 <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	181 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	182 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	183 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	184 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	185 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	186 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	187 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	188 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	189 <param name="type" value="scatter" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	190 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	191 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	192 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	193 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	194 <output name="output" ftype="txt" file="scatter.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	195 <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	196 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	197 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	198 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	199 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	200 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	201 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	202 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	203 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	204 <param name="type" value="dispersion" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	205 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	206 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	207 <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	208 <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	209 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	210 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	211 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	212 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	213 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	214 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	215 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	216 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	217 <param name="type" value="scatterMatrix" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	218 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	219 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	220 <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	221 <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	222 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	223 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	224 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	225 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	226 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	227 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	228 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	229 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	230 <param name="type" value="pca" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	231 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	232 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	233 <output name="output" ftype="txt" file="pca.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	234 <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	235 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	236 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	237 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	238 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	239 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	240 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	241 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	242 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	243 <param name="type" value="expressionplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	244 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	245 <param name="gene_id" value="XLOC_000059" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	246 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	247 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	248 <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	249 <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	250 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	251 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	252 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	253 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	254 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	255 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	256 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	257 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	258 <param name="features" value="gene" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	259 <param name="type" value="expressionbarplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	260 <param name="gene_id" value="XLOC_000039" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	261 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	262 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	263 <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	264 <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	265 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	266 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	267 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	268 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	269 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	270 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	271 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	272 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	273 <param name="type" value="heatmap" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	274 <repeat name="genes">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	275 <param name="gene_id" value="XLOC_000078" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	276 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	277 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	278 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	279 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	280 <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	281 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	282 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	283 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	284 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	285 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	286 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	287 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	288 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	289 <param name="type" value="density" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	290 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	291 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	292 <output name="output" ftype="txt" file="density.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	293 <discovered_dataset designation="density-0" ftype="png" file="density.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	294 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	295 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	296 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	297 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	298 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	299 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	300 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	301 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	302 <param name="type" value="dendrogram" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	303 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	304 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	305 <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	306 <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	307 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	308 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	309 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	310 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	311 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	312 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	313 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	314 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	315 <param name="type" value="volcano" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	316 <param name="x" value="q1" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	317 <param name="y" value="q2" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	318 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	319 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	320 <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	321 <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	322 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	323 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	324 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	325 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	326 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	327 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	328 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	329 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	330 <param name="type" value="boxplot" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	331 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	332 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	333 <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	334 <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	335 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	336 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	337 <test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	338 <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	339 <repeat name="plots">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	340 <param name="width" value="1280" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	341 <param name="height" value="960" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	342 <conditional name="plot">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	343 <param name="type" value="fpkmSCV" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	344 </conditional>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	345 </repeat>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	346 <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	347 <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	348 </output>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	349 </test>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	350 </tests>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	351 <help><![CDATA[
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	352 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.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	353 ------
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	354 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	355 ]]></help>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	356 <citations>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	357 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	358 </citations>
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper. devteam parents: diff changeset	359 </tool>

Mercurial > repos > devteam > cummerbund

annotate cummeRbund.xml @ 2:ac2ebc60ef5d draft