Mercurial > repos > stemcellcommons > scdetools

annotate scde_list_match.xml @ 0:b1d730728d5f default tip

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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 <?xml version="1.0"?>
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2 <tool id="scde-list-match" name="SCDE ListMatch" version="1.0" hidden="false">
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3 <description>match a list against one or more selected reference gene lists</description>
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4 <version_string>scde --version</version_string>
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5
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6 <command interpreter="perl">
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7 scde match --source $source
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8 --organism $organism
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9
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10 #if str($symbol_type) != ""
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11 --symbol $symbol_type
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12 #end if
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13
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14 #if $query.type == "file"
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15 --file $query.filename
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16 --column $query.column
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17 #else
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18 $query.source
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19 #end if
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20 --min-matches $min_matches
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21 --output $format
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22
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23 #if str($output_html) != "None"
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24 > $output_html
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25 #else
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26 > $output_tab
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27 #end if
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28 </command>
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29
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30 <inputs>
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31 <param name="source" type="select" label="Compare your gene list to">
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32 <option value="wikipathways">Wikipathways</option>
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33 <option value="genesigdb">GeneSigDB</option>
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34 <option value="msigdb">MSigDB</option>
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35 <option value="scd">SCDE Repository - Public</option>
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36 </param>
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37
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38 <param name="organism" type="select" label="Query Organism" help="Which organism did your gene list come from?">
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39 <option value="human">Human</option>
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40 <option value="mouse">Mouse</option>
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41 </param>
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42
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43 <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with.">
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44 <option value="symbol">Gene Symbol</option>
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45 <option value="ensembl">Ensembl ID</option>
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46 <option value="entrez">Entrez ID</option>
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47 </param>
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48
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49 <conditional name="query">
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50 <param name="type" type="select" label="Query source" help="You may select a file from your User History or enter a list of genes as text.">
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51 <option value="file">History File</option>
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52 <option value="text">Enter Text</option>
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53 </param>
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54
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55 <when value="file">
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56 <param name="filename" format="txt" type="data" label="Query History File" help="Select a file from your History"/>
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57 <param name="column" type="data_column" data_ref="filename" label="Query File Column Number" help="Column numbers start at 1. Verify that the column number corresponds to the Gene ID Type you specified."/>
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58 </when>
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59
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60 <when value="text">
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61 <param name="source" type="text" area="true" size="5x60" label="Query using Text Entry" help="Paste a list of gene symbols here, separated by a space, tab, new line or a comma."/>
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62 </when>
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63 </conditional>
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64
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65 <param name="min_matches" type="select" label="Minimum Number of Matches" help="Select the minimum number of genes that must be matched per reference gene list.">
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66 <option value="1">1</option>
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67 <option value="2">2</option>
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68 <option value="3">3</option>
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69 <option value="4">4</option>
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70 <option value="5">5</option>
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71 </param>
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72
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73 <param name="format" type="select" label="Output Format" help="Select the format for the output file.">
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74 <option value="html">HTML</option>
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75 <option value="tab">Tab Delimited</option>
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76 </param>
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77 </inputs>
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78
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79 <outputs>
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80 <data format="html" name="output_html">
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81 <filter>format == "html"</filter>
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82 </data>
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83 <data format="tabular" name="output_tab">
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84 <filter>format == "tab"</filter>
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85 </data>
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86 </outputs>
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87
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88 <help>
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89 **What it does**
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90
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91 This tool compares a list of genes as a query against one or more selected reference lists.
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92
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93 -----
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94
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95 .. class:: infomark
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96
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97 Please upload your data as a tab-delimited text file. If the column number does not appear as a dropdown menu, make sure the file type is 'Tabular'.
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98
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99 -----
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100
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101 **Screencast!**
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102
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103 Watch the SCDE ListMatch Screencast_ (right click to open this link in another window).
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104
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105 .. _Screencast: http://discovery.hsci.harvard.edu/screencasts/galaxy.html
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106 </help>
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107 </tool>