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author Ilya Sytchev <isytchev@hsph.harvard.edu>
date Mon, 07 Oct 2013 18:54:25 -0400
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1 <tool id="scde-list-compare" name="SCDE ListCompare" version="1.0" hidden="false">
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2 <description>compare multiple lists against one or more selected reference lists</description>
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3 <version_string>scde --version</version_string>
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4
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5 <command interpreter="perl">
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6 scde compare --source $source
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7
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8 #for $i in $lists
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9 --file ${i.filename}
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10 --column ${i.column}
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11 --organism ${i.organism}
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12 --symbol ${i.symbol_type}
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13 #end for
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14 --output $format
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15
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16 #if str($output_html) != "None"
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17 > $output_html
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18 #else
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19 > $output_tab
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20 #end if
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21 </command>
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22
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23 <inputs>
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24 <param name="source" type="select" label="Compare your gene lists to">
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25 <option value="wikipathways">Wikipathways</option>
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26 <option value="genesigdb">GeneSigDB</option>
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27 <option value="msigdb">MSigDB</option>
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28 <option value="scd">SCDE Repository - Public</option>
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29 </param>
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30
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31 <repeat name="lists" title="Add List" min="2" >
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32 <param name="filename" type="data" format="txt" label="Dataset" help="Select a list for comparison from your History." />
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33
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34 <param name="column" type="select" label="Gene Column" help="Select the column number corresponding to the gene identifier">
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35 <option value="1">c1</option>
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36 <option value="2">c2</option>
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37 <option value="3">c3</option>
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38 <option value="4">c4</option>
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39 <option value="5">c5</option>
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40 <option value="6">c6</option>
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41 <option value="7">c7</option>
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42 <option value="8">c8</option>
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43 <option value="9">c9</option>
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44 <option value="10">c10</option>
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45 </param>
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46
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47 <param name="organism" type="select" label="Query Organism" help="Which organism do your gene lists come from?">
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48 <option value="human">Human</option>
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49 <option value="mouse">Mouse</option>
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50 </param>
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51
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52 <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with.">
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53 <option value="symbol">Gene Symbol</option>
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54 <option value="ensembl">Ensembl ID</option>
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55 <option value="entrez">Entrez ID</option>
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56 </param>
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57 </repeat>
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58
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59 <param name="format" type="select" label="Output Format" help="Select the Format for the Output File">
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60 <option value="html">HTML</option>
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61 <option value="tab">Tab Delimited</option>
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62 </param>
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63 </inputs>
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64
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65 <outputs>
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66 <data format="html" name="output_html">
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67 <filter>format == "html"</filter>
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68 </data>
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69 <data format="tabular" name="output_tab">
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70 <filter>format == "tab"</filter>
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71 </data>
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72 </outputs>
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73
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74 <help>
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75 **What it does**
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76
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77 This tool compares two or more sets of gene lists against one or more selected reference lists.
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78
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79 -----
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80
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81 .. class:: infomark
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82
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83 Upload data in tabular format to your history using the "Get Data" -> "Upload File" tool.
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84
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85 .. class:: infomark
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86
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87 Additional lists may be added using the "Add new List" button.
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88 </help>
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89 </tool>
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90