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annotate cummeRbund.xml @ 0:e462121e8269 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:27:38 -0500
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e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <?xml version="1.0"?>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <tool id="cummeRbund" name="cummeRbund" version="1.0.1">
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3 <description>visualize Cuffdiff output</description>
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4 <requirements>
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5 <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="package" version="2.8.2">cummeRbund</requirement>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 </requirements>
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9 <expand macro="stdio" />
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10 <macros>
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11 <import>cummeRbund_macros.xml</import>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 </macros>
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13 <code file="cummeRbund_options.py"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 <command>
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15 <![CDATA[
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16 #for i, p in enumerate($plots):
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args
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18 --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
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19 --outfile plot-${p.plot.type}-${i}.png
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
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21 $p.plot.replicates
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22 #elif $p.plot.type == "scatter":
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23 $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
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24 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
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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
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26 #for gene in $p.plot.multiple_genes.genes:
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27 --genes ${gene.gene_id}
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28 #end for
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29 #end if
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30 #elif $p.plot.type == "maplot":
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31 --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
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32 #elif $p.plot.type == "volcano":
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33 --x "$p.plot.x" --y "$p.plot.y"
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34 #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
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35 --features $p.plot.multiple_genes.features --gene_selector
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36 #for gene in $p.plot.multiple_genes.genes:
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 --genes ${gene.gene_id}
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38 #end for
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39 #end if
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40 #elif $p.plot.type == "heatmap":
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41 --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 #if len($p.plot.genes) > 0:
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43 #for gene in $p.plot.genes:
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44 --genes ${gene.gene_id}
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45 #end for
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46 #end if
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47 #elif $p.plot.type == "cluster":
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48 --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
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49 #if len($p.plot.genes) > 0:
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50 #for gene in $p.plot.genes:
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51 --genes ${gene.gene_id}
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52 #end for
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53 #end if
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54 #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
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55 #if $p.plot.type == "expressionplot":
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56 $p.plot.draw_summary
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57 #end if
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58 --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
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59 #end if
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60 #if $p.plot.type == "density":
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61 $p.plot.log10
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62 #end if
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63 > "${output}" 2>&1 ;
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64 #end for
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65 ]]></command>
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66 <inputs>
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67 <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
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68 <repeat name="plots" title="Plots">
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69 <param name="width" type="integer" value="1280" label="The width of the image"/>
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70 <param name="height" type="integer" value="960" label="The height of the image"/>
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71 <conditional name="plot">
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72 <param name="type" type="select" label="Plot type">
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73 <option value="density" selected="true">Density</option>
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74 <option value="boxplot">Boxplot</option>
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75 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
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76 <option value="pca">Principal Component Analysis (PCA) Plot</option>
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77 <option value="dendrogram">Dendrogram</option>
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78 <option value="scatter">Scatter</option>
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79 <option value="volcano">Volcano</option>
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80 <option value="heatmap">Heatmap</option>
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81 <option value="dispersion">Dispersion</option>
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82 <option value="fpkmSCV">Squared Coefficient of Variation</option>
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83 <option value="scatterMatrix">Scatter Matrix</option>
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84 <option value="cluster">Cluster</option>
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85 <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
86 <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
87 <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
88 </param>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
89 <when value="density">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
90 <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
91 <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
92 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
93 <when value="mds">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
94 <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
95 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
96 <when value="pca">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
97 <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
98 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
99 <when value="boxplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
100 <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
101 <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
102 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
103 <when value="dendrogram">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
104 <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
105 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
106 <when value="scatter">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
107 <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
108 <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
109 <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
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diff changeset
110 <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
111 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
112 <when value="volcano">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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)" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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114 <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
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diff changeset
115 <expand macro="multiple_genes_conditional" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
116 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
117 <when value="heatmap">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
118 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
119 <expand macro="genes_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
120 <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
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diff changeset
121 <option value="row">Row</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
122 <option value="column">Column</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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123 <option value="both" selected="true">Both</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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124 <option value="none">None</option>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
125 </param>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
126 <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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127 <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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128 <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
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diff changeset
129 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
130 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
131 <when value="cluster">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
132 <expand macro="features_selector" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
133 <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
134 <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
135 <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
136 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
137 <when value="maplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
138 <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
139 <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
140 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
141 <when value="dispersion" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
142 <when value="fpkmSCV" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
143 <when value="scatterMatrix" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
144 <when value="expressionplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
145 <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
146 <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
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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?"/>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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148 <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
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diff changeset
149 <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
150 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
151 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
152 <when value="expressionbarplot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
153 <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
154 <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
155 <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
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parents:
diff changeset
156 <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
157 <expand macro="log10_checkbox" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
158 </when>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
159 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
160 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
161 </inputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
162 <outputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
163 <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
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diff changeset
164 <discover_datasets pattern="plot-(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
165 </data>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
166 </outputs>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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167 <tests>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
168 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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169 <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
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parents:
diff changeset
170 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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171 <param name="width" value="1280" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
172 <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
173 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
174 <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
175 <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
176 <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
177 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
178 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
179 <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
180 <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
181 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
182 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
183 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
184 <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
185 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
186 <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
187 <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
188 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
189 <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
190 <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
191 <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
192 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
193 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
194 <output name="output" ftype="txt" file="scatter.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
195 <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
196 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
197 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
198 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
199 <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
200 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
201 <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
202 <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
203 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
204 <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
205 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
206 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
207 <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
208 <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
209 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
210 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
211 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
212 <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
213 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
214 <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
215 <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
216 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
217 <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
218 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
219 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
220 <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
221 <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
222 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
223 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
224 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
225 <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
226 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
227 <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
228 <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
229 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
230 <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
231 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
232 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
233 <output name="output" ftype="txt" file="pca.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
234 <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
235 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
236 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
237 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
238 <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
239 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
240 <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
241 <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
242 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
243 <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
244 <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
245 <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
246 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
247 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
248 <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
249 <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
250 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
251 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
252 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
253 <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
254 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
255 <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
256 <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
257 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
258 <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
259 <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
260 <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
261 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
262 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
263 <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
264 <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
265 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
266 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
267 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
268 <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
269 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
270 <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
271 <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
272 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
273 <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
274 <repeat name="genes">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
275 <param name="gene_id" value="XLOC_000078" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
276 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
277 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
278 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
279 <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
280 <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
281 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
282 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
283 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
284 <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
285 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
286 <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
287 <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
288 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
289 <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
290 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
291 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
292 <output name="output" ftype="txt" file="density.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
293 <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
294 </output>
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 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
297 <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
298 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
299 <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
300 <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
301 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
302 <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
303 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
304 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
305 <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">
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="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
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="volcano" />
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
316 <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
317 <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
318 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
319 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
320 <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
321 <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
322 </output>
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 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
325 <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
326 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
327 <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
328 <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
329 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
330 <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
331 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
332 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
333 <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
334 <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
335 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
336 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
337 <test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
338 <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
339 <repeat name="plots">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
340 <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
341 <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
342 <conditional name="plot">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
343 <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
344 </conditional>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
345 </repeat>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
346 <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
347 <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
348 </output>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
349 </test>
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
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350 </tests>
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351 <help><![CDATA[
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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.
e462121e8269 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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353
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354 ------
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355
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356 Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
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357 ]]></help>
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358 <citations>
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359 <citation type="doi">doi:10.1038/nprot.2012.016</citation>
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360 </citations>
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361 </tool>