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1 <tool id="tabular2HTML" name="Tabular-to-HTML" version="1.0.0">
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2 <description>for easier table viewing</description>
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3 <command interpreter="perl">
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4 tabular2HTML.pl
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5 $tableHeader
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6 $input
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7 $output
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8 #if $headerSource.source == 'explicit':
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9 #for $header in $headerSource.headers
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10 #if len($header.subheaders) > 0
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11 ${len($header.subheaders)}
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12 #else
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13 1
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14 #end if
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15 #end for
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16 #end if
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17 </command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Tabular data"/>
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20 <conditional name="headerSource">
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21 <param name="source" type="select" label="Header">
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22 <option value="numbers">Column numbers</option>
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23 <option value="names">Column names (if available)</option>
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24 <option value="explicit">Specify headers and subheaders</option>
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25 <option value="none">None</option>
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26 </param>
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27 <when value="numbers">
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28 </when>
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29 <when value="names">
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30 </when>
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31 <when value="explicit">
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32 <repeat name="headers" title="Header">
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33 <param name="name" type="text" label="Name">
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34 <sanitizer>
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35 <valid initial="string.printable">
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36 <remove value="<"/>
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37 <remove value=">"/>
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38 </valid>
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39 <mapping initial="none">
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40 <add source="<" target="&lt;"/>
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41 <add source=">" target="&gt;"/>
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42 </mapping>
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43 </sanitizer>
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44 </param>
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45 <repeat name="subheaders" title="Subheader">
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46 <param name="name" type="text" label="Name"/>
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47 </repeat>
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48 </repeat>
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49 </when>
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50 <when value="none">
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
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55 <data format="html" name="output"/>
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56 </outputs>
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57 <configfiles>
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58 <configfile name="tableHeader">
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59 <html><head><style type="text/css">
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60 table,td,th
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61 {
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62 border: 1px solid #dddddd;
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63 border-collapse: collapse;
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64 padding: 4px;
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65 font-size: 10pt;
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66 }
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67 th{border-width:2px; background-color: #888888; color: #ffffff}
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68 tr.odd {background-color: #f2fff2}
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69 tr.even {background-color: #f2f2ff}
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70 td.darkRight {border-right: 2px solid #888888}
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71 </style></head><body>
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72 <table style="border-collapse:collapse">
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73 #if $headerSource.source == 'numbers':
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74 <tr>
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75 #for $i in range(int($input.metadata.columns)):
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76 <th>${i + 1}</th>
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77 #end for
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78 </tr>
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79 #elif $headerSource.source == 'names' and hasattr($input.datatype, 'column_names'):
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80 <tr>
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81 #for $columnName in $input.datatype.column_names:
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82 <th>$columnName</th>
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83 #end for
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84 </tr>
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85 #elif $headerSource.source == 'explicit':
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86 <tr>
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87 #for $header in $headerSource.headers:
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88 <th
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89 #if len($header.subheaders) > 0:
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90 colspan="${len($header.subheaders)}"
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91 #else
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92 rowspan="2"
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93 #end if
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94 >
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95 $header.name
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96 </th>
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97 #end for
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98 <tr>
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99 #for $header in $headerSource.headers:
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100 #for $subheader in $header.subheaders:
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101 <th>
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102 ${subheader.name}
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103 </th>
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104 #end for
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105 #end for
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106 </tr>
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107 #end if
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108 </configfile>
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109 </configfiles>
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110 <help>
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111 **===What it does===**
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112
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113 Wraps tabular data in an HTML table for easier viewing.
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114
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115 ------
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116
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117 **===Headers===**
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118
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119 **Column numbers** - The header will show the order of the columns.
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120
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121 **Column names** - The header will show column names if the data file is a
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122 specific type of tabular file that has column names in
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123 Galaxy (such as *sam* or *taxonomy*). Otherwise, no header will be shown.
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124
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125 **Specify headers and subheaders** - This allows custom headers, which can span
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126 multiple columns if subheaders are included. For example, the tabular file::
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127
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128 1 2 3 4
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129 read1 100 12345 50
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130 read2 150 56789 60
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131
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132 ...with the headers and subheaders::
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133
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134 Query
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135 ID
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136 length
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137 Hit
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138 gi
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139 score
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140
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141 ...would create an html table with the format:
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142
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143 +----------------+---------------+
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144 | Query | Hit |
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145 +-------+--------+-------+-------+
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146 | ID | length | gi | score |
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147 +=======+========+=======+=======+
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148 | read1 | 100 | 12345 | 50 |
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149 +-------+--------+-------+-------+
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150 | read2 | 150 | 56789 | 60 |
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151 +-------+--------+-------+-------+
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152
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153 </help>
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154 </tool>
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