Mercurial > repos > iuc > raceid_clustering

annotate macros_inspectclusters.xml @ 0:4ea021bd7513 draft

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author iuc
date Thu, 22 Nov 2018 04:43:57 -0500
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <macros>
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2 <macro name="inspectclusters_inputs" >
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3 <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the cluster analysis" />
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4 <conditional name="plotgen">
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5 <param name="do_opt" type="select" label="Plot All Clusters?" help="Generates tSNE and F-R plots" >
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6 <option value="yes" selected="true" >Yes</option>
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7 <option value="no" >No</option>
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8 </param>
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9 <when value="no" />
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10 <when value="yes" />
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11 </conditional>
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12 <conditional name="plotsym" >
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13 <param name="do_opt" type="select" label="Perform Subset Analysis?" >
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14 <expand macro="yesno_checkedno" />
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15 </param>
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16 <when value="no" />
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17 <when value="yes">
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18 <param name="types_regex" type="text" optional="true" label="Types Regex (removal)" help="Regular expression to be used to remove portions of the cell names, in order to indicate cell type. e.g. if your cells are labelled as 'cdk5_1, cdk5_2, glow_1, glow_2', then a regex of '_\\d$' would trim off the ends and set the cell types to 'cdk5, cdk5, glow, glow'. " >
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19 <expand macro="sanitize_regex" />
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20 </param>
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21 <expand macro="use_defaults_no" >
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22 <param name="subset_regex" type="text" optional="true" label="Subset of Types: Regex (select)" help="Regular expression to be used to select for cell types of interest. e.g. if we are only interested in 'cdk5' positive cells, then we would simply put 'cdk5' here. ">
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23 <expand macro="sanitize_regex" />
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24 </param>
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25 <param name="fr" type="boolean" checked="false" label="Output FR map instead of tSNE" help="Performs a Fruchterman-Rheingold projection instead of tSNE" />
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26 </expand>
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27 </when>
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28 </conditional>
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29 <conditional name="gois" >
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30 <param name="do_opt" type="select" label="Examine Genes of Interest" >
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31 <expand macro="yesno_checkedno" />
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32 </param>
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33 <when value="no" />
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34 <when value="yes">
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35 <param name="inspect_goi_genes" type="text" value="" label="Genes to Examine" >
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36 <expand macro="sanitize_string_vector" />
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37 </param>
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38 <param name="inspect_goi_cells" type="text" optional="true" label="Cells to Examine" help="Leave blank to examine all" ><!-- "":NULL -->
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39 <expand macro="sanitize_string_vector" />
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40 </param>
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41 <expand macro="use_defaults_no" >
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42 <!-- Yes, examine genes of interest, but no do not use defaults... -->
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43 <param name="inspect_goi_imputed" type="boolean" checked="false" label="Impute Genes" help="Only works if k-nearest neighbours was used in the clustering" />
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44 <param name="plotexp_n" type="text" optional="true" label="Title of plot" help="If blank, the list of genes are used" >
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45 <expand macro="sanitize_title" />
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46 </param>
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47 <param name="plotmarkg_cthr" type="integer" min="0" value="0" label="Cluster Threshold" help="Include only clusters with cells greater than this" />
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48 <param name="plotmarkg_cl" type="text" optional="true" label="Cluster List" help="List of cluster numbers to include. Leave blank to include all" >
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49 <expand macro="sanitize_numeric_vector" />
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50 </param><!-- "":NULL -->
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51 <param name="plotmarkg_order_cells" type="boolean" checked="false" label="Order Cells" help="Order heatmap by cell names, not by cluster" />
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52 <param name="plotmarkg_aggr" type="boolean" checked="false" label="Average Expression" help="Show only average expression for each cluster" />
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53 <param name="plotmarkg_norm" type="boolean" checked="false" label="Normalise Gene Expression " help="Normalise gene expression to 1 to depict genes on the same scale" />
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54 <param name="plotmarkg_flo" type="integer" max="-5" optional="true" label="Lower-bound for Gene Expression" /><!-- negative or null vals only for this seem to work-->
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55 <param name="plotmarkg_cap" type="integer" min="1" optional="true" label="Upper-bound for Gene Expression" />
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56 <param name="plotmarkg_samples" type="text" optional="true" label="Regex to Select Sample Names For Each cell" >
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57 <expand macro="sanitize_regex" />
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58 </param>
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59 <param name="plotmarkg_cluster_cols" type="boolean" checked="false" label="Cluster columns" />
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60 <param name="plotmarkg_cluster_rows" type="boolean" checked="true" label="Cluster rows" />
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61 <param name="plotmarkg_cluster_set" type="boolean" checked="false" label="Order Clusters by Heirarchal Clustering of Cluster Medoids." />
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62 </expand>
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63 </when>
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64 </conditional>
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65 <conditional name="diffgtest" >
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66 <param name="do_opt" type="select" label="Differential Gene Testing" >
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67 <expand macro="yesno_checkedno" />
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68 </param>
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69 <when value="no" />
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70 <when value="yes" >
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71 <expand macro="select_cells" sectionname="set_a" sectiontitle="Cells in Set A" />
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72 <expand macro="select_cells" sectionname="set_b" sectiontitle="Cells in Set B" />
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73 <expand macro="use_defaults_no" >
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74 <param name="plotdiffg_pthr" type="float" min="0" max="1" value="0.05" label="P-value cutoff" help="Cutoff for displaying differentially expressed genes" />
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75 <param name="plotdiffg_padj" type="boolean" checked="true" label="Apply B-H Correction" help="Display genes with a Benjamini-Hochberg corrected false discovery rate lower than the above P-value threshold" />
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76 <param name="plotdiffg_lthr" type="float" min="0" value="0" label="Log2-Fold Threshold" help="Differentially expressed genes are displayed only for log2 fold-changes higher than this" />
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77 <param name="plotdiffg_mthr" type="float" optional="true" label="Log2 Mean Threshold" help="Differentially expressed genes are displayed only for log2 mean expression greater than this" /><!-- opt:-Inf -->
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78 <param name="plotdiffg_show_names" type="boolean" checked="false" label="Display Gene Names" />
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79 </expand>
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80 </when>
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81 </conditional>
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82 </macro>
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83 <macro name="inspectclusters_tests" >
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84 <test><!-- general plots, plotgen -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
85 <param name="inputrds" value="out_cluster_default.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
86 <conditional name="plotgen" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
87 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
88 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
89 <output name="outpdf" value="out_cluster_general_default.pdf" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
90 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
91 <test><!-- default test, plotsym -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
92 <param name="inputrds" value="out_cluster_default.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
93 <conditional name="plotsym" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
94 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
95 <param name="types_regex" value="\\_\\d+" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
96 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
97 <param name="subset_regex" value="IV|V" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
98 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
99 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
100 <conditional name="gois" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
101 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
102 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
103 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
104 <output name="outpdf" value="out_cluster_inspect_default.pdf" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
105 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
106 <test><!-- Advanced 1 -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
107 <param name="inputrds" value="out_cluster_default.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
108 <conditional name="plotsym" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
109 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
110 <param name="types_regex" value="\\_\\d+" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
111 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
112 <param name="subset_regex" value="IV|V" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
113 <param name="fr" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
114 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
115 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
116 <conditional name="gois" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
117 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
118 <param name="inspect_goi_genes" value="Apoa1,Apoa1bp,Apoa2,Apoa4,Apoa5" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
119 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
120 <param name="inspect_goi_imputed" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
121 <param name="plotexp_n" value="Test Title" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
122 <param name="plotmarkg_order_cells" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
123 <param name="plotmarkg_aggr" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
124 <param name="plotmarkg_norm" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
125 <param name="plotmarkg_flo" value="-10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
126 <param name="plotmarkg_cap" value="100" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
127 <param name="plotmarkg_samples" value="(\\_\\d+)$" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
128 <param name="plotmarkg_cluster_cols" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
129 <param name="plotmarkg_cluster_rows" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
130 <param name="plotmarkg_cluster_set" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
131 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
132 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
133 <conditional name="diffgtest" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
134 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
135 <section name="set_a" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
136 <param name="name_set" value="Test set A" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
137 <conditional name="meth" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
138 <param name="type" value="regex" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
139 <param name="selector" value="^V5.*" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
140 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
141 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
142 <section name="set_b" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
143 <param name="name_set" value="Test set B" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
144 <conditional name="meth" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
145 <param name="type" value="manual" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
146 <param name="selector" value="I5d_3,I5d_4,I5d_6,I5d_8,I5d_9,I5d_10,I5d_11,I5d_12,I5d_13,I5d_14" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
147 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
148 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
149 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
150 <param name="plotdiffg_pthr" value="0.1" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
151 <param name="plotdiffg_padj" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
152 <param name="plotdiffg_lthr" value="0.2" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
153 <param name="plotdiffg_mthr" value="0.2" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
154 <param name="plotdiffg_show_names" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
155 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
156 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
157 <output name="outpdf" value="out_cluster_inspect_advanced1.pdf" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
158 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
159 <test><!-- Advanced 2 -->
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
160 <param name="inputrds" value="out_cluster_default.rdat" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
161 <conditional name="plotsym" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
162 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
163 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
164 <param name="fr" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
165 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
166 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
167 <conditional name="gois" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
168 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
169 <param name="inspect_goi_genes" value="Sp1,Spc24,Spcs1,Spcs2,Spcs3" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
170 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
171 <param name="plotexp_n" value="Test Title 2" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
172 <param name="plotmarkg_order_cells" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
173 <param name="plotmarkg_aggr" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
174 <param name="plotmarkg_norm" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
175 <param name="plotmarkg_flo" value="-10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
176 <param name="plotmarkg_cap" value="10" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
177 <param name="plotmarkg_cluster_cols" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
178 <param name="plotmarkg_cluster_rows" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
179 <param name="plotmarkg_cluster_set" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
180 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
181 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
182 <conditional name="diffgtest" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
183 <param name="do_opt" value="yes" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
184 <section name="set_a" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
185 <param name="name_set" value="Test set A" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
186 <conditional name="meth" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
187 <param name="type" value="regex" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
188 <param name="selector" value="^IV.*" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
189 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
190 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
191 <section name="set_b" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
192 <param name="name_set" value="Test set B" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
193 <conditional name="meth" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
194 <param name="type" value="cln" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
195 <param name="selector" value="3" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
196 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
197 </section>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
198 <expand macro="test_nondef" >
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
199 <param name="plotdiffg_pthr" value="0.8" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
200 <param name="plotdiffg_padj" value="true" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
201 <param name="plotdiffg_lthr" value="0.8" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
202 <param name="plotdiffg_mthr" value="0.8" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
203 <param name="plotdiffg_show_names" value="false" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
204 </expand>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
205 </conditional>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
206 <output name="outpdf" value="out_cluster_inspect_advanced2.pdf" />
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
207 </test>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
208 </macro>
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
209 <token name="@INSPECTCLUSTERS_CHEETAH@"><![CDATA[
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
210
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
211 in.rdat = readRDS('${inputrds}')
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
212
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
213 perform.plotting = FALSE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
214 perform.symbolmap = FALSE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
215 perform.genesofinterest = FALSE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
216 perform.diffgene = FALSE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
217
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
218 #if str($plotgen.do_opt) == "yes":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
219 perform.plotting = TRUE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
220 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
221
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
222 #if str($plotsym.do_opt) == "yes":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
223 perform.symbolmap = TRUE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
224 plotsym = formals(plotsymbolsmap)
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
225 plotsym.use.typeremoveregex = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
226 plotsym.use.typeremoveregex.subselect = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
227 plotsym.use.typeremoveregex = as.character( '$plotsym.types_regex' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
228 #if str($plotsym.use.def) == "no":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
229 plotsym\$fr = as.logical( '$plotsym.use.fr' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
230 #if $plotsym.use.subset_regex:
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
231 plotsym.use.typeremoveregex.subselect = as.character( '$plotsym.use.subset_regex' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
232 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
233 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
234 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
235
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
236 #if str($gois.do_opt) == "yes":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
237 perform.genesofinterest = TRUE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
238 plotexp = formals(plotexpmap)
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
239 plotmarkg = formals(plotmarkergenes)
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
240
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
241 inspect.goi.use.genes = string2textvector( '$gois.inspect_goi_genes' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
242 plotexp\$g = inspect.goi.use.genes
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
243 plotmarkg\$genes = inspect.goi.use.genes
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
244
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
245 #if $gois.inspect_goi_cells:
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
246 inspect.goi.use.cells = as.character( '$gois.inspect_goi_cells' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
247 plotexp\$cells = inspect.goi.use.cells
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
248 plotmarkg\$cells = inspect.goi.use.cells
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
249 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
250 #if str($gois.use.def) == "no":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
251 inspect.goi.use.imputed = as.logical( '$gois.use.inspect_goi_imputed' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
252 plotexp\$imputed = inspect.goi.use.imputed
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
253 plotmarkg\$imputed = inspect.goi.use.imputed
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
254 #if $gois.use.plotmarkg_cl
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
255 plotmarkg\$cl = string2numericvector( '$gois.use.plotmarkg_cl' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
256 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
257 #if $gois.use.plotmarkg_cap
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
258 plotmarkg\$cap = as.integer( '$gois.use.plotmarkg_cap' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
259 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
260 #if $gois.use.plotmarkg_flo
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
261 plotmarkg\$flo = as.integer( '$gois.use.plotmarkg_flo' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
262 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
263 #if $gois.use.plotmarkg_samples
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
264 plotmarkg\$samples = as.character( '$gois.use.plotmarkg_samples' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
265 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
266 #if $gois.use.plotexp_n
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
267 plotexp\$n = as.character( '$gois.use.plotexp_n' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
268 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff changeset
269 plotmarkg\$cthr = as.integer( '$gois.use.plotmarkg_cthr' )
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270 plotmarkg\$order.cells = as.logical( '$gois.use.plotmarkg_order_cells' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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271 plotmarkg\$aggr = as.logical( '$gois.use.plotmarkg_aggr' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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272 plotmarkg\$norm = as.logical( '$gois.use.plotmarkg_norm' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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273 plotmarkg\$cluster_cols = as.logical( '$gois.use.plotmarkg_cluster_cols' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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274 plotmarkg\$cluster_rows = as.logical( '$gois.use.plotmarkg_cluster_rows' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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275 plotmarkg\$cluster_set = as.logical( '$gois.use.plotmarkg_cluster_set' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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276 #end if
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277 #end if
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278
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279 #if str($diffgtest.do_opt) == "yes":
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280 plotdiffg = formals(plotdiffgenesnb)
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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281
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282 perform.diffgene = TRUE
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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283 plotdiffg\$Aname = '$diffgtest.set_a.name_set'
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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284 plotdiffg\$Bname = '$diffgtest.set_b.name_set'
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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285
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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286 gfdat.A.use = list()
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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287 gfdat.B.use = list()
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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288
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289 gfdat.A.use\$manual = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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290 gfdat.A.use\$regex = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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291 gfdat.A.use\$cln = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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292 gfdat.B.use\$manual = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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293 gfdat.B.use\$regex = NULL
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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294 gfdat.B.use\$cln = NULL
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295
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296 #if str($diffgtest.set_a.meth.type) == "cln":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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297 gfdat.A.use\$cln = c( '$diffgtest.set_a.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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298 #else if str($diffgtest.set_a.meth.type) == "regex":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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299 gfdat.A.use\$regex = as.character( '$diffgtest.set_a.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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300 #else if str($diffgtest.set_a.meth.type) == "manual":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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301 gfdat.A.use\$manual = string2textvector( '$diffgtest.set_a.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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302 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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303
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304 #if str($diffgtest.set_b.meth.type) == "cln":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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305 gfdat.B.use\$cln = c( '$diffgtest.set_b.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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306 #else if str($diffgtest.set_b.meth.type) == "regex":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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307 gfdat.B.use\$regex = as.character( '$diffgtest.set_b.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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308 #else if str($diffgtest.set_b.meth.type) == "manual":
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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309 gfdat.B.use\$manual = string2textvector( '$diffgtest.set_b.meth.selector' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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310 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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311
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312 #if str($diffgtest.use.def) == "no":
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313 plotdiffg\$pthr = as.numeric( '$diffgtest.use.plotdiffg_pthr' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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314 plotdiffg\$padj = as.logical( '$diffgtest.use.plotdiffg_padj' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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315 plotdiffg\$lthr = as.integer( '$diffgtest.use.plotdiffg_lthr' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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316 plotdiffg\$show_names = as.logical( '$diffgtest.use.plotdiffg_show_names' )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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317 #if $diffgtest.use.plotdiffg_mthr
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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318 plotdiffg\$mthr = as.numeric( '$diffgtest.use.plotdiffg_mthr' )
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319 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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320 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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321 #end if
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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322
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323 out.pdf='${outpdf}'
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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324 ]]>
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325 </token>
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326 </macros>