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annotate pathifier.xml @ 1:0960bd1161fa draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
author artbio
date Mon, 12 Feb 2024 23:57:01 +0000
parents fec313f5c889
children
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0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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1 <tool id="pathifier" name="Pathifier" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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2 <description>: Quantify deregulation of pathways in cancer</description>
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0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.40.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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6 <token name="@PROFILE@">23.0</token>
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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7 </macros>
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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8 <requirements>
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0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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9 <requirement type="package" version="@TOOL_VERSION@">bioconductor-pathifier</requirement>
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10 <requirement type="package" version="1.7.4">r-optparse</requirement>
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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11 <requirement type="package" version="1.0.12">r-pheatmap</requirement>
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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12 <requirement type="package" version="0.3_44">r-scatterplot3d</requirement>
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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13 <requirement type="package" version="0.4.15">r-circlize</requirement>
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fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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14 </requirements>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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15 <stdio>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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16 <exit_code range="1:" level="fatal" description="Tool exception" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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17 </stdio>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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18 <command detect_errors="exit_code"><![CDATA[
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0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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19 Rscript '$__tool_directory__/pathifier.R'
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20 --exp '$input'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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21 --sep '$input_sep'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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22 --genes '$genes'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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23
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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24 #if str($reference.reference_selector) == 'TRUE':
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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25 --is_normal '$reference.reference_selector'
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26 --normals '$reference.normals'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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27 #end if
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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29 --max_stability '$max_stability'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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30 --attempts '$attempts'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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31 --min_std '$min_std'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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32 --min_exp '$min_exp'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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33
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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34 --heatmap_cluster_cells '$heatmap_cluster_cells'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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35 --heatmap_cluster_pathways '$heatmap_cluster_pathways'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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36 --heatmap_show_cell_labels '$heatmap_show_cell_labels'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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37 --heatmap_show_pathway_labels '$heatmap_show_pathway_labels'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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38
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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39 --pds '$pds'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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40 --logfile '$logfile'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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41 --plot '$plot'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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42 --rdata '$rdatafile'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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43 ]]></command>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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44 <inputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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45 <param name="input" type="data" format="txt,tabular" label="expression data"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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46 <param name="input_sep" type="select" label="Input column separator">
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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47 <option value="tab" selected="true">Tabs</option>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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48 <option value=",">Comma</option>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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49 </param>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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50 <param name="genes" type="data" format="txt" label="Gene sets Pathways"
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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51 help="Must be in gmt format (one pathway per line : Name, description, genes (one by column), tab separated)" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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52 <conditional name="reference">
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
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53 <param name="reference_selector" label="Do you have non cancer transcriptomes in your data set ?" type="select"
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54 help="Yes, if the starting curve depends on the matrix of points with in a certain row order
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55 (first 'normal' then 'cancer' samples), otherwise (No) the first principal component is used. See help section for more informations">
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56 <option selected="True" value="TRUE">Yes</option>
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57 <option value="">No</option>
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58 </param>
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59 <when value="TRUE">
0
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60 <param name="normals" type="data" format="tabular" label="Sample status"
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61 help="A two-column data frame, first column contains data labels, second column the levels of sample status : 1 = Healthy, 0 = Tumor (no header)" />
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62 </when>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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63 <when value="">
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64 </when>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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65 </conditional>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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66 <param name="max_stability" label="Throw away components leading to low stability of sampling noise" type="boolean" truevalue="TRUE"
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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67 falsevalue="FALSE" checked="true" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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68 <param name="attempts" type="integer" label="Number of runs to determine stability" value="100"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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69 <param name="min_std" type="text" value="0.4" label="Minimum of standard deviation to filter out low variable genes"
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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70 help="Use 'data' to use the minimum standard deviation of your data" />
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71 <param name="min_exp" type="text" value="4" label="Minimum of gene expression to filter out low variable genes"
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72 help="Use 'data' to use the minimum expression of your data" />
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73 <param name="heatmap_cluster_cells" label="Cluster samples on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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74 <param name="heatmap_cluster_pathways" label="Cluster pathways on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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75 <param name="heatmap_show_cell_labels" label="Show sample labels on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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76 <param name="heatmap_show_pathway_labels" label="Cluster pathway labels on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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77 <param label="Return log file of pathifier" name="log" type="select" >
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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78 <option value="no" selected="True">No</option>
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79 <option value="yes">Yes</option>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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80 </param>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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81 <param label="Return Pathifier S4 object" name="rdata" type="select" >
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82 <option value="no" selected="True">No</option>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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83 <option value="yes">Yes</option>
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84 </param>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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85 </inputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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86 <outputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
87 <data name="pds" format="tabular" label="Pathifier Deregulation Score (PDS) of ${on_string}" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
88 <data name="logfile" format="txt" label="Pathifier log file of ${on_string}" >
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
89 <filter>log == 'yes'</filter>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
90 </data>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
91 <data name="plot" format="pdf" label="Pathifier vizualization of ${on_string}" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
92 <data name="rdatafile" format="rdata" label="Pathifier S4 object of ${on_string}" >
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
artbio
parents: 0
diff changeset
93 <filter>rdata == 'yes'</filter>
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
94 </data>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
95 </outputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
96 <tests>
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
artbio
parents: 0
diff changeset
97 <test expect_num_outputs="3">
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
98 <param name="input" value="sheffer.tsv" ftype="tabular"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
99 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
artbio
parents: 0
diff changeset
100 <param name="reference_selector" value="TRUE" />
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
101 <param name="normals" value="normals.tsv" ftype="tabular" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
102 <param name="log" value="yes" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
103 <param name="attempts" value="100" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
104 <output name="logfile" file="sheffer.kegg.log" ftype="txt" compare="sim_size" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
105 <output name="pds" file="sheffer.kegg.tsv" ftype="tabular"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
106 <output name="plot" file="plot.pdf" ftype="pdf" compare="sim_size" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
107 </test>
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
artbio
parents: 0
diff changeset
108 <test expect_num_outputs="3">
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
109 <param name="input" value="sheffer_noref.tsv" ftype="tabular"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
110 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
1
0960bd1161fa planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier commit f7363f7c391bd501fc4d1c10aaf372ec2bd82732
artbio
parents: 0
diff changeset
111 <param name="reference_selector" value="" />
0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
112 <param name="log" value="no" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
113 <param name="rdata" value="yes" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
114 <param name="attempts" value="50" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
115 <param name="min_exp" value="data" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
116 <param name="min_std" value="data" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
117 <output name="pds" file="sheffer.kegg_noref.tsv" ftype="tabular"/>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
118 <output name="rdatafile" file="sheffer.kegg_noref.rdata" ftype="rdata" compare="sim_size" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
119 <output name="plot" file="plot_noref.pdf" ftype="pdf" compare="sim_size" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
120 </test>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
121 </tests>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
122 <help>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
123
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
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124 **What it does**
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
125
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
126 Pathifier is an algorithm that infers pathway deregulation scores for each (tumor) sample on the basis
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
127 of expression data. This score is determined, in a context-specific manner, for every particular dataset
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
128 and type of cancer that is being investigated. The algorithm transforms gene-level information into
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
129 pathway-level information, generating a compact and biologically relevant representation of each sample.
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
130
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
131 For each pathway analysed, the transcriptome datasets are plotted in the gene pathway space using a
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
132 Principal Component analysis (PCA) and a principal curve is regressed from these points. All transcriptomes
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
133 are projected on the nearest point of this curve. Pathifier finally computes a score which corresponds to
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
134 the distance (normalized to 1) of each point (transcriptome) to the curve origin.
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
135
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
136 **Inputs**
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
137
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
138 * a matrix of n columns of observations (generally RNAseq experiments) and k rows of variables (generally k genes).
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
139 * a Gene Matrix Transposed file (GMT format) where each row represents a gene set :
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
140 * first column : gene set name (pathway name)
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
141 * second : description of gene set
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
142 * third and + : list of genes that composed the gene set tab-separated
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
143 * (Optional) a two column table with no header, to described transcriptome status (Tumor or not) :
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
144 * first column : sample labels
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
145 * second : levels of sample status : 1 = Healthy, 0 = Tumor
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
146
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
147 **Outputs**
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
148
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
149 * Table of Pathway Deregulation Scores : one by pathway (column) and by transcriptome (row)
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
150 * Visualization of PDS (pdf) :
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
151 * Principal curve of different PDS
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
152 * Heatmap of PDS that allows (through clustering) to see pattern in pathway deregulation
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
153 * (Optional) Log file of Pathifier algorithm
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
154 * (Optional) Pathifier S4 object which contains all informations and results generated by Pathifier, for each pathway :
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
155 * `scores` : PDS scores
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
156 * `genesinpathway` : Gene identifiers in each pathway
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
157 * `newmeanstd`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
158 * `origmeanstd`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
159 * `pathwaysize` : Number of genes retained in pathway
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
160 * `curves` : Coordinates of transcriptomes projected on the principal curve
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
161 * `curves_order` : Order of transcriptomes along the principal curve
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
162 * `z` : z-scores matrix
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
163 * `compin`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
164 * `xm`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
165 * `xs`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
166 * `center`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
167 * `rot`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
168 * `pctaken` : Number of principal component retained for pathifier analysis
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
diff changeset
169 * `samplings`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
170 * `sucess` : List of pathway index that passed Pathfiier filters (more info in log file)
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
171 * `logfile` : Name of logfile
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
172
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
173 </help>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
174 <citations>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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175 <citation type="bibtex">@Manual{,
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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176 title = {{pathifier}: Quantify deregulation of pathways in cancer},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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177 author = {Yotam Drier},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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178 year = {2013-06-27},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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179 note = {R package version 1.22.0},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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180 url = {https://git.bioconductor.org/packages/pathifier},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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181 }
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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182 </citation>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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183 <citation type="bibtex">@article {Drier6388,
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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184 author = {Drier, Yotam and Sheffer, Michal and Domany, Eytan},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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185 title = {Pathway-based personalized analysis of cancer},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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186 volume = {110},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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187 number = {16},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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188 pages = {6388--6393},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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189 year = {2013},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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190 doi = {10.1073/pnas.1219651110},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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191 publisher = {National Academy of Sciences},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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192 issn = {0027-8424},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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193 URL = {https://www.pnas.org/content/110/16/6388},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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194 eprint = {https://www.pnas.org/content/110/16/6388.full.pdf},
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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195 journal = {Proceedings of the National Academy of Sciences}
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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196 }
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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197 </citation>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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198 </citations>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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199 </tool>