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annotate pathway_image.xml @ 23:66a183c44dd5

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bugfix for Pathway Image tool
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 22 May 2013 15:58:18 -0400
parents d6b961721037
children a631c2f6d913
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66a183c44dd5 bugfix for Pathway Image tool
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1 <tool id="gd_pathway_image" name="Pathway Image" version="1.1.0">
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2 <description>: Draw a KEGG pathway, highlighting specified gene modules</description>
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3
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4 <command interpreter="python">
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5 mkpthwpng.py
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6 "--input=${input}"
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7 "--output=${output}"
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8 "--KEGGpath=${pathway}"
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9 "--posKEGGclmn=${kpath}"
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10 "--KEGGgeneposcolmn=${kgene}"
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11 </command>
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12
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Dataset" />
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15 <param name="kgene" type="data_column" data_ref="input" label="Column with KEGG gene ID" />
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16 <param name="kpath" type="data_column" data_ref="input" numerical="false" label="Column with KEGG pathways" />
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17 <param name="pathway" label="Pathway" type="select">
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18 <options from_file="gd.pathways.txt">
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19 <column name="value" index="1"/>
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20 <column name="name" index="2"/>
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21 <filter type="data_meta" ref="input" key="dbkey" column="0" separator="\t" />
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22 </options>
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23 </param>
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24 </inputs>
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25
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26 <outputs>
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27 <data name="output" format="png" />
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="input" value="test_in/sample.gd_sap" ftype="gd_sap" />
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33 <param name="kpath" value="10" />
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34 <param name="kgene" value="12" />
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35 <param name="pathway" value="cfa05214" />
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36 <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" />
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37 </test>
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38 </tests>
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39
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40 <help>
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41
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42 **Dataset formats**
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43
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44 The input and output datasets are in tabular_ format.
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45 The input dataset must have columns with KEGG gene ID and pathways.
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46 The output dataset is described below.
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47 (`Dataset missing?`_)
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48
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49 .. _tabular: ./static/formatHelp.html#tab
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50 .. _Dataset missing?: ./static/formatHelp.html
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51
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52 -----
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53
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54 **What it does**
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55
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56 This tool produces an image of a KEGG pathway, highlighting (in red) the
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57 modules representing genes in the input dataset. Click here_ for help
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58 with reading the pathway map.
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59
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60 NOTE: a given gene can
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61 be assigned to multiple modules, and different genes can be assigned to
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62 the same module.
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63
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64 .. _here: http://www.genome.jp/kegg/document/help_pathway.html
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65
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66 -----
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67
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68 **Example**
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69
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70 - input::
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71
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72 476153 probably damaging cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
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73 483960 probably damaging N
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74 610160 possibly damaging N
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75 403657 benign cfa04010=MAPK signaling pathway.cfa04012=ErbB signaling pathway.cfa04060=Cytokine-cytokine receptor interaction.cfa04144=Endocytosis.cfa04510=Focal adhesion.cfa04540=Gap junction.cfa04810=Regulation of actin cytoskeleton.cfa05160=Hepatitis C.cfa05200=Pathways in cancer.cfa05212=Pancreatic cancer.cfa05213=Endometrial cancer.cfa05214=Glioma.cfa05215=Prostate cancer.cfa05218=Melanoma.cfa05219=Bladder cancer.cfa05223=Non-small cell lung cancer
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76 etc.
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77
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78 output showing pathway cfa05214:
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79
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80 .. image:: ${static_path}/images/gd_pathway_image.png
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81
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82 </help>
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83 </tool>