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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="2014-09-16">cistrome</requirement>
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5 </requirements>
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6 </xml>
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7 <xml name="requirements_bx">
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8 <requirements>
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9 <requirement type="package" version="2014-09-16">cistrome</requirement>
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10 <requirement type="package" version="0.7.1">bx-python</requirement>
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11 </requirements>
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12 </xml>
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13 <xml name="stdio">
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14 <stdio>
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15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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16 <exit_code range="1:" level="fatal" description="Error" />
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17 </stdio>
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18 </xml>
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19 <xml name="ceasdb_ref">
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20 <conditional name="ref">
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21 <param name="refsrc" type="select" label="">
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22 <option value="cached">cached</option>
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23 <option value="history">history</option>
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24 <!--
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25 <option value="build">build</option>
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26 -->
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27 </param>
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28 <when value="cached">
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29 <param name="ceasdb" type="select" label="">
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30 <options from_data_table="ceasdb">
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31 <filter type="unique_value" column="0" />
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32 </options>
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33 </param>
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34 </when>
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35 <when value="history">
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36 <param name="gdb" type="data" format="ceasdb" label="Gene annotation table file (sqlite3)"/>
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37 </when>
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38 <!--
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39 <when value="build">
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40 </when>
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41 -->
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42 </conditional>
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43 </xml>
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44
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45 <template name="script_chars">
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46 #set global $dollar = chr(36)
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47 #set global $gt = chr(62)
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48 #set global $lt = chr(60)
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49 #set global $ad = chr(38)
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50 </template>
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51
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52 <template name="gtpath_ceasdb_ref">
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53 #if $ref.refsrc == 'history':
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54 -g $ref.gdb
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55 #elif $ref.refsrc == 'cached':
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56 -g $ref.ceasdb.fields.path
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57 ## #elif $ref.refsrc == 'build':
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58 ## #else:
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59 ## -g os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "ceaslib", "GeneTable", $dbkey )
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60 #end if
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61 </template>
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62 <template name="validate_bedfile_sh">
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63 ##check line count and file format accuracy of bed file
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64 lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'`
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65 ## bypass validation for now
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66 ## format=`$path/validation/fcfunc.py $bfile`
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67 format="passed"
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68 if [[ ${dollar}lines -gt 100000 ]];then
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69 echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2
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70 exit;
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71 fi
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72 if [[ ${dollar}format != "passed" ]]; then
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73 echo ${dollar}format ${gt}${ad}2
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74 exit;
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75 fi
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76 </template>
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77
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78 <token name="@EXTERNAL_DOCUMENTATION@">
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79
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80 For details about this application, please go to:
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81 http://liulab.dfci.harvard.edu/CEAS/usermanual.html
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82
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83 Prebuilt reference Gene annotation tables (SQLite3) are available at:
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84 http://liulab.dfci.harvard.edu/CEAS/download.html
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85 http://liulab.dfci.harvard.edu/CEAS/src/
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86
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87 Set the dataset datatype to: "ceasdb" when uploading to your history.
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88
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89 </token>
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90 <token name="@CITATION_SECTION@">------
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91
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92 **Citation**
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93
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94 For the underlying tool, please cite the following publication:
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95 "CEAS: cis-regulatory element annotation system", Hyunjin Shin, Tao Liu, Arjun K. Manrai, and X. Shirley Liu,
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96 Bioinformatics. 2009 Oct 1;25(19):2605-6. doi: 10.1093/bioinformatics/btp479. Epub 2009 Aug 18.
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97
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98 </token>
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99 </macros>
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