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annotate pathifier.xml @ 0:fec313f5c889 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
author artbio
date Mon, 12 Apr 2021 09:55:24 +0000
parents
children 0960bd1161fa
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0
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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1 <tool id="pathifier" name="Pathifier" version="1.0.1">
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>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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3 <requirements>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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4 <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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5 <requirement type="package" version="1.22.0=r351_0">bioconductor-pathifier</requirement>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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6 <requirement type="package" version="1.0.12=r351h6115d3f_0">r-pheatmap</requirement>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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7 <requirement type="package" version="0.3_41=r351h6115d3f_0">r-scatterplot3d</requirement>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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8 <requirement type="package" version="0.4.7=r35h6115d3f_0">r-circlize</requirement>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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9 </requirements>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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10 <stdio>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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11 <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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12 </stdio>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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13 <command detect_errors="exit_code"><![CDATA[
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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14 Rscript $__tool_directory__/pathifier.R
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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15 --exp '$input'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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16 --sep '$input_sep'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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17 --genes '$genes'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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18
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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19 #if $reference.is_normal == "Yes":
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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20 --is_normal 'TRUE'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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21 --normals '$reference.normals'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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22 #end if
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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23
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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24 --max_stability '$max_stability'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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25 --attempts '$attempts'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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26 --min_std '$min_std'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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27 --min_exp '$min_exp'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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28
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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29 --heatmap_cluster_cells '$heatmap_cluster_cells'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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30 --heatmap_cluster_pathways '$heatmap_cluster_pathways'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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31 --heatmap_show_cell_labels '$heatmap_show_cell_labels'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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32 --heatmap_show_pathway_labels '$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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33
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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34 --pds '$pds'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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35 --logfile '$logfile'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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36 --plot '$plot'
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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37 --rdata '$rdatafile'
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 ]]></command>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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40 <inputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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41 <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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42 <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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43 <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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44 <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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45 </param>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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46 <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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47 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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48 <conditional name="reference">
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49 <param name="is_normal" label="Do you have non cancer transcriptomes in your data set ?" type="boolean" truevalue="Yes" falsevalue="" checked="false"
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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50 help="If set the starting curve depends on the matrix of points with in a certain row order (first 'normal' then 'cancer' samples), otherwise the first principal component is used. See help for more informations"/>
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51 <when value="Yes">
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52 <param name="normals" type="data" format="tabular" label="Sample status"
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53 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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54 </when>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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55 <when value="">
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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56 </when>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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57 </conditional>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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58 <param name="max_stability" label="Throw away components leading to low stability of sampling noise" type="boolean" truevalue="TRUE"
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59 falsevalue="FALSE" checked="true" />
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60 <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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61 <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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62 help="Use 'data' to use the minimum standard deviation of your data" />
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63 <param name="min_exp" type="text" value="4" label="Minimum of gene expression 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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64 help="Use 'data' to use the minimum expression of your data" />
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65 <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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66 <param name="heatmap_cluster_pathways" label="Cluster pathways on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" />
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67 <param name="heatmap_show_cell_labels" label="Show sample labels on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
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68 <param name="heatmap_show_pathway_labels" label="Cluster pathway labels on heatmap" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" />
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69 <param label="Return log file of pathifier" name="log" type="select" >
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70 <option value="no" selected="True">No</option>
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71 <option value="yes">Yes</option>
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72 </param>
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73 <param label="Return Pathifier S4 object" name="rdata" type="select" >
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74 <option value="no" selected="True">No</option>
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75 <option value="yes">Yes</option>
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76 </param>
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77
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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78 </inputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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79 <outputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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80 <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"
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81 <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"
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82 <filter>log == 'yes'</filter>
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83 </data>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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84 <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"
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85 <data name="rdatafile" format="rdata" label="Pathifier S4 object of ${on_string}" >
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
86 <filter>rds == 'yes'</filter>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
87 </data>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
88 </outputs>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
89 <tests>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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90 <test>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
91 <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
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diff changeset
92 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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93 <param name="is_normal" value="True" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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94 <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
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95 <param name="log" value="yes" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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96 <param name="attempts" value="100" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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97 <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
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98 <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
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99 <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
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100 </test>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
parents:
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101 <test>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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102 <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
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diff changeset
103 <param name="genes" value="kegg_pathways.gmt" ftype="txt" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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104 <param name="is_normal" value="" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
105 <param name="log" value="no" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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106 <param name="rdata" value="yes" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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107 <param name="attempts" value="50" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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108 <param name="min_exp" value="data" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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109 <param name="min_std" value="data" />
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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110 <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
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diff changeset
111 <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
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diff changeset
112 <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
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113 </test>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
114 </tests>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
115 <help>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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116
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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117 **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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118
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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119 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
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120 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
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121 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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122 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
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123
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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124 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
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125 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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126 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
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diff changeset
127 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
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diff changeset
128
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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129 **Inputs**
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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130
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
131 * 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
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132 * 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
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133 * 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
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134 * 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
135 * 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
136 * (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:
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137 * 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
138 * 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
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139
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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140 **Outputs**
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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141
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
142 * 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
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143 * Visualization of PDS (pdf) :
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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144 * Principal curve of different PDS
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
145 * 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
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diff changeset
146 * (Optional) Log file of Pathifier algorithm
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
147 * (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
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148 * `scores` : PDS scores
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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149 * `genesinpathway` : Gene identifiers in each pathway
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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150 * `newmeanstd`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
151 * `origmeanstd`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
152 * `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
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153 * `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
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diff changeset
154 * `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
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155 * `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
156 * `compin`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
157 * `xm`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
158 * `xs`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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diff changeset
159 * `center`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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160 * `rot`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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161 * `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
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162 * `samplings`
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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163 * `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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164 * `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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165
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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166 </help>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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167 <citations>
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
artbio
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168 <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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169 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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170 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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171 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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172 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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173 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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174 }
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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175 </citation>
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176 <citation type="bibtex">@article {Drier6388,
fec313f5c889 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier commit b94cfc7bf8df30aa8e9249b75ea31332ee2bada1"
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177 author = {Drier, Yotam and Sheffer, Michal and Domany, Eytan},
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178 title = {Pathway-based personalized analysis of cancer},
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179 volume = {110},
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180 number = {16},
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181 pages = {6388--6393},
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182 year = {2013},
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183 doi = {10.1073/pnas.1219651110},
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184 publisher = {National Academy of Sciences},
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185 issn = {0027-8424},
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186 URL = {https://www.pnas.org/content/110/16/6388},
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187 eprint = {https://www.pnas.org/content/110/16/6388.full.pdf},
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188 journal = {Proceedings of the National Academy of Sciences}
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189 }
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190 </citation>
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191 </citations>
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192 </tool>