Mercurial > repos > iuc > raceid_diffgene

annotate raceid_diffgenes.xml @ 0:d6a18fea319f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:33:01 -0500
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d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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1 <tool id="raceid_diffgene" name="RaceID differential gene expression analysis" version="@VERSION@.0">
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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2 <description>Identify differentially regulated genes</description>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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3 <macros>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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4 <import>macros.xml</import>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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5 </macros>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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6 <expand macro="requirements" />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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7 <command detect_errors="exit_code"><![CDATA[
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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8 Rscript '@SCRIPT_DIR@/raceID_diffgenes.R' '@SCRIPT_DIR@' '$rconf_source'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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9
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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10 #if $compare_clusters_select.do_compare_clusters.value == "T":
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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11 &&
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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12 mkdir '${out_html.files_path}' &&
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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13 mv plot_*.svg '${out_html.files_path}' &&
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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15 echo '<html><head></head>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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16 <body>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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17 <h1>RaceID Differential Gene Analysis</h1>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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18 <br /><h3>Expression of ${compare_clusters_select.gene} between ${compare_clusters_select.cl1} and ${compare_clusters_select.cl2}</h3>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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19 <img src="plot_diffgenes.svg" ><br />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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20 </body>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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21 </html>' > '$out_html'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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22 #end if
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23
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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24 ]]></command>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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25
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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26 <configfiles>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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27 <configfile name="rconf_source" >
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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28 sc = readRDS( '$inp_rdat' )
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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29
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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30 c_pval = as.numeric( '$pval' )
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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31 generate_extable = as.logical( '$gen_gexpr_table.value' )
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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32 outtable_dir = 'tables'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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33 compare_clusters = as.logical( '$compare_clusters_select.do_compare_clusters.value' )
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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34
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35 #if $compare_clusters_select.do_compare_clusters.value == "T":
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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36 gene_name = '$compare_clusters_select.gene'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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37 clust1 = '$compare_clusters_select.cl1'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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38 clust2 = '$compare_clusters_select.cl2'
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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39 mcount = as.integer( '$compare_clusters_select.mincount' )
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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40 #end if
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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41 </configfile>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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42 </configfiles>
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43
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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44 <inputs>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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45 <param name="inp_rdat" type="data" format="rdata" label="Count matrix with clusters" help="This file is the output of the RaceID pipeline." />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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46 <param name="pval" type="float" value="0.01" min="1e-10" max="0.5" label="Retain genes with p-value smaller than threshold" help="The p-value for observing the difference in mean expression between the cluster and all cells based on binomial counting statistics." />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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47 <param name="gen_gexpr_table" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Generate table of all differentially expressed genes?" />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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48 <conditional name="compare_clusters_select">
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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49 <param name="do_compare_clusters" type="select" label="Compare the expression of a specific gene between two sets of clusters?" >
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50 <option value="T" >Yes</option>
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51 <option value="F" selected="true" >No</option>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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52 </param>
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53 <when value="F" />
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54 <when value="T" >
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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55 <param name="gene" type="text" label="Gene name of interest" >
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56 <sanitizer invalid_char="" >
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57 <valid initial="string.letters,string.digits">
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58 <add value="_"/><add value="+" /><add value="-" />
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59 </valid>
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60 </sanitizer>
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61 </param>
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62 <param name="cl1" type="text" value="1" label="Cluster set 1" help="e.g. if you wish to compare cluster 2 to clusters 1 and 3, then type '2' here and '1,3' in the next input." >
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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63 <sanitizer invalid_char="" >
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64 <valid initial="string.digits"><add value="," /></valid>
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65 </sanitizer>
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66 </param>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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67 <param name="cl2" type="text" value="2" label="Cluster set 2" help="You can also compare sets of clusters to one another: e.g. 1,4,5 against 2,3." >
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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68 <sanitizer invalid_char="" >
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69 <valid initial="string.digits"><add value="," /></valid>
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70 </sanitizer>
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71 </param>
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72 <param name="mincount" type="integer" value="5" min="1" label="Only count genes with more than this number of transcripts in at least one cell within Cluster set 1 or Cluster set 2" />
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73 </when>
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74 </conditional>
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75 </inputs>
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76
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77 <outputs>
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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78 <data name="out_html" format="html" label="${tool.name} on ${on_string}: Web Report" />
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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79 <data format="tsv" name="out_tables" label="${tool.name} on ${on_string}: DiffExpr Tables" >
d6a18fea319f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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80 <discover_datasets pattern="__designation_and_ext__" directory="tables" visible="true" />
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81 </data>
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82 </outputs>
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83
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84 <tests>
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85 <test>
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86 <param name="inp_rdat" value="in_diffgene.rdat" />
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87 <output name="out_html" value="out_diffgene1.html" />
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88 <!-- verify just two of the outputs -->
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89 <output name="out_tables" >
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90 <!-- Problems here... help appreciated -->
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91 <discovered_dataset designation="gdiff_cl.1" ftype="tsv" file="gdiff_cl.1.tsv" />
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92 <discovered_dataset designation="gdiff_cl.2" ftype="tsv" file="gdiff_cl.2.tsv" />
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93 </output>
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94 </test>
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95 <test>
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96 <!-- Diff Cluster plot only -->
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97 <param name="inp_rdat" value="in_diffgene.rdat" />
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98 <param name="pval" value="0.05" />
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99 <param name="gen_gexpr_table" value="F" />
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100 <param name="do_compare_clusters" value="T" />
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101 <param name="gene" value="1110038F14Rik__chr15" />
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102 <param name="cl1" value="1" />
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103 <param name="cl2" value="2,3" />
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104 <param name="mincount" value="2" />
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105 <output name="out_html" value="out_diffgene2.html" />
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109 *****************
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110 RaceID Diff Genes
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111 *****************
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112
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113 Generates a table of all differentially expressed genes, and a plot representing the expression of a specific gene of interest between different clusters.
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114
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115 The RaceID pipeline must be run prior to using this tool, as the input of this tool is generated from the output of the pipeline.
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116
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117
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>