Mercurial > repos > iuc > genomic_super_signature

annotate genomic_super_signature.xml @ 0:d0cbe6cc1f04 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
author iuc
date Wed, 12 Jan 2022 19:07:45 +0000
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d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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1 <tool id="genomic_super_signature" name="GenomicSuperSignature" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.01">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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2 <description>interpretation of RNAseq experiments</description>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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3 <macros>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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4 <token name="@TOOL_VERSION@">1.2.0</token>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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5 <token name="@GALAXY_VERSION@">0</token>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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6 </macros>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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7 <requirements>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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8 <requirement type="package" version="@TOOL_VERSION@">bioconductor-genomicsupersignature</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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9 <requirement type="package" version="1.7.1">r-optparse</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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10 <requirement type="package" version="2.6">r-wordcloud</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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11 <requirement type="package" version="2.22.0">bioconductor-biocstyle</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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12 <requirement type="package" version="2.7.3">r-magick</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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13 <requirement type="package" version="2021d">tzdata</requirement>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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14 </requirements>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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15 <command detect_errors="exit_code"><![CDATA[
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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16 #set $model = $model.fields.path
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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17 mkdir out &&
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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18 Rscript '$__tool_directory__/gss.R' --input '$input' --model '$model' --method '$method' --maxFrom '$maxFrom' --level '$level' --scale '$scale' --numOut $numOut --outDir out --toolDir '$__tool_directory__' --validate '$validate' --html '$html'
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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19 ]]></command>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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20 <inputs>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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21 <param argument="--input" type="data" format="tabular,tsv" label="Tabular count matrix"/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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22 <param argument="--model" type="select" label="Using RAVmodel" help="Select model from the list">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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23 <options from_data_table="genomic_super_signature_ravmodels">
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24 <filter type="data_meta" ref="input" key="dbkey" column="dbkey" />
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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25 </options>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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26 <validator type="no_options" message="A built-in RAVmodel is not available for the build associated with the selected input file"/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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27 </param>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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28 <param argument="--method" type="select" label="Select a correlation coefficient">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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29 <option value="pearson">Pearson</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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30 <option value="kendall">Kendall</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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31 <option value="spearman">Spearman</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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32 </param>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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33 <param argument="--maxFrom" type="select" label="Select whether to display the maximum value from dataset's PCs or avgLoadings" help="With Principal Component (PC), the maximum correlation coefficient from top 8 PCs for each avgLoading will be selected as an output. If you choose Average Loading, the Average Loading with the maximum correlation coefficient with each Principal Component will be in the output.">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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34 <option value="pc">Principal Components</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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35 <option value="avgLoading">Average Loading</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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36 </param>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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37 <param argument="--level" type="select" label="Output format of validated result" help="max will output the matrix containing only the maximum coefficient. To get the coefficient of all 8 PCs, set this argument to all.">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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38 <option value="max">Max</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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39 <option value="all">All</option>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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40 </param>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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41 <param argument="--scale" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Normalize rows of datasets?"/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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42 <param argument="--numOut" type="integer" min="1" value="3" label="The number of top validated RAVs to check"/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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43 </inputs>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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44 <outputs>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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45 <collection name="genesets" type="list" label="GenomicSuperSignature Genesets">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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46 <discover_datasets pattern=".*_genesets_(?P&lt;name&gt;.+)\.csv" format="csv" directory="out" />
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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47 </collection>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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48 <collection name="literatures" type="list" label="GenomicSuperSignature Literatures">
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49 <discover_datasets pattern=".*_literatures_(?P&lt;name&gt;.+)\.csv" format="csv" directory="out" />
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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50 </collection>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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51 <data name="validate" format="csv" label="GenomicSuperSignature validate.csv">
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52 </data>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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53 <data name="html" format="html" label="GenomicSuperSignature report.html">
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54 </data>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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55 </outputs>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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56 <tests>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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57 <test>
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58 <param name="input" value="bcellViperExpr_10C.tsv.gz" dbkey="hg38" ftype="tabular"/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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59 <param name="model" value="microRAVmodel" dbkey="hg38"/>
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60 <param name="method" value="Pearson"/>
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61 <param name="maxFrom" value="Principal Components"/>
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62 <param name="level" value="Max"/>
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63 <param name="numOut" value="1"/>
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64 <output name="html" ftype="html">
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65 <assert_contents>
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66 <has_n_lines n="2843"/>
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67 </assert_contents>
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68 </output>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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69 <output name="validate" ftype="csv">
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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70 <assert_contents>
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71 <has_line line='"","score","PC","sw","cl_size","cl_num"'/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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72 <has_text text='"RAV1076"'/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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73 <has_text text='"RAV725"'/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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74 <has_text text='"RAV884"'/>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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75 <has_text text='"RAV1994"'/>
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76 <has_n_lines n="5"/>
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77 </assert_contents>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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78 </output>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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79 </test>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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diff changeset
80 </tests>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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81 <help><![CDATA[
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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82 GenomicSuperSignature
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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83 =====================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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84
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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85 What it does
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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86 ------------
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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parents:
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87
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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88 Connect new gene expression profile with the relevant information from
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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diff changeset
89 the existing databases, such as previous publications, MeSH terms, and
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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90 gene sets.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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91
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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92 Inputs
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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93 ------
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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94
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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95 Count Files
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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96 ~~~~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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97
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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98 GenomicSuperSignature takes a count matrix as an input. Input file
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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99 should have row names in gene symbols and column names in sample ID. For
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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100 the best result, we recommend a data transformation (e.g. log2) for the
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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101 input to follow a normal distribution, while scaling is NOT recommended.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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102 Currently for validation, inputs need at least eight samples.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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103
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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104 Example of input format:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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105
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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106 ===== ======== ========= ======== =========
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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107 \ GSM44075 GSM44078 GSM44080 GSM44081
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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108 ===== ======== ========= ======== =========
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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109 ADA 9.571369 10.599436 8.740659 10.104469
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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110 CDH2 6.175890 5.312704 5.651928 4.462205
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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111 MED6 9.671113 8.773383 9.190276 9.526235
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
parents:
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112 NR2E3 9.847733 9.582061 9.628792 8.820422
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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113 ===== ======== ========= ======== =========
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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114
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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115 RAVmodel
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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116 ~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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117
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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118 *R*\ eplicable *A*\ xes of *V*\ ariation (RAV) consists of principal
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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119 components repeatedly observed in an independent analysis of multiple
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
iuc
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120 published datasets. RAVs connect different databases that are both
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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121 linked to the originated study or associated with the RAV itself through
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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122 the gene rankings of it. RAVmodel contains the collection of RAVs
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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123 (RAVindex), metadata from model building process and the additional
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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124 annotations. Currently, two RAVmodels are available based on the gene
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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125 sets used for annotation.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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126
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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127 1) C2 : RAVmodel annotated with Molecular Signatures Database (MSigDB)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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128 curated gene sets (version 7.1)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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129 2) PLIERpriors : RAVmodel annotated with the three gene sets provided in
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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130 the `PLIER package <https://github.com/wgmao/PLIER>`__ -
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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131 bloodCellMarkersIRISDMAP, svmMarkers, and canonicalPathways
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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132
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133 Outputs
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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134 -------
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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135
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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136 There are four categories of outputs from this tool, which is one html
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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137 file and three csv tabular files. The actual number of csv files will
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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138 vary depending on the parameter, *–numOut*, and the validated RAVs.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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139
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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140 validate.csv
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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141 ~~~~~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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142
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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143 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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144 | Column | Description |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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145 +==========================+============================================+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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146 | score | the maximum pearson correlation |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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147 | | coefficient between the top 8 PCs of the |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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148 | | input and RAVs |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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149 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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150 | PC | one of the top 8 PCs of the input, which |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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151 | | gives the highest *score* |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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152 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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153 | sw | the average silhouette width of the RAV |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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154 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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155 | cl_size | the size of each RAV |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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156 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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157 | cl_num | the RAV number |
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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158 +--------------------------+--------------------------------------------+
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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159
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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160 Genesets
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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161 ~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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162
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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163 This is the enriched gene sets for the target RAV, calculated from the
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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164 ranked gene list. Gene sets with the adjusted p-value < 0.05 are
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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165 included.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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166
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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167 =========== ================================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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168 Column Description
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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169 =========== ================================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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170 Description name of the gene sets
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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171 NES normalized enrichment score (ES)
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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172 pvalue statistical significance
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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173 qvalues p-value adjusted for the FDR
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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174 =========== ================================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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175
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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176 Literatures
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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177 ~~~~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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178
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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179 ========= ======================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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180 Column Description
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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181 ========= ======================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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182 studyName study accession
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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183 title the title of the study
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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184 ========= ======================
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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185
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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186 report.html
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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187 ~~~~~~~~~~~
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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188
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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189 A html file with the summary of the main analyses by
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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190 GenomicSuperSignature. It includes MeSH terms in word cloud and an
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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191 interactive plot overviewing the validated RAVs, in addition to the
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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192 previews of the tabular output files.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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193
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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194 Citations
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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195 ---------
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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196
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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197 Oh, S., Geistlinger, L., Ramos, M., Taroni, J.N., Carey, V.J., Greene,
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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198 C.S., Waldron, L., & Davis, S.R. (2021). GenomicSuperSignature:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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199 interpretation of RNA-seq experiments through robust, efficient
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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200 comparison to public databases. bioRxiv.
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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201
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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202 References
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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203 ----------
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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204
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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205 | GenomicSuperSignature package:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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206 `webpage <https://shbrief.github.io/GenomicSuperSignature/>`__
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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207 | GenomicSuperSignature usecases:
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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208 `webpage <https://shbrief.github.io/GenomicSuperSignaturePaper/>`__
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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209 ]]></help>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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210 <citations>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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211 <citation type="doi">10.1101/2021.05.26.445900</citation>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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212 </citations>
d0cbe6cc1f04 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
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213 </tool>